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/7775247/working' mkdir: created directory `/scratch/stefan/7775247/working/protonate' Storing results in /scratch/stefan/7775247/finished Working in /scratch/stefan/7775247/working /scratch/stefan/7775247/working /scratch/stefan/7775247 /scratch/stefan/7775247/working/protonate /scratch/stefan/7775247/working /scratch/stefan/7775247 Precomputing protomers for all compounds (pH: 7.4) Dec 01, 2019 12:06:45 AM java.util.prefs.FileSystemPreferences syncWorld WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException: Couldn't get file lock. ph 7.4: 1014 protomers created Coalesing and merging protomers 1005 protomers generated for 1000 compounds Checking for new stereocenters and expanding 1006 protomers after new stereo-center expansion /scratch/stefan/7775247/working /scratch/stefan/7775247 Bulk generating 3D conformations all protomers in /scratch/stefan/7775247/working/3D mkdir: created directory `/scratch/stefan/7775247/working/3D' We are using corina for 3D embeding debuging info:: /scratch/stefan/7775247/working/protonate/xaaabjj-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' 1007 3D conformations generated for 1000 compounds Building REAL300004919001 mkdir: created directory `/scratch/stefan/7775247/working/building' mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919001' /scratch/stefan/7775247/working/building/REAL300004919001 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919001 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919001/0 /scratch/stefan/7775247/working/building/REAL300004919001 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/1 `/scratch/stefan/7775247/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCOC1=CC=C(Cl)C=C1)C(=O)[O-]) `REAL300004919001.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919001 none CC#CCC(NC(=O)CCCOC1=CC=C(Cl)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 82, 82, 28, 82, 18, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 116, 158, 158, 201, 201, 201, 201, 201, 116, 82, 28, 28, 18, 18, 8, 8, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 1072 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919001 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919001 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 mkdir: created directory `/scratch/stefan/7775247/finished' Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919001/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919001 Building REAL300004919002 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919002' /scratch/stefan/7775247/working/building/REAL300004919002 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919002 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919002/0 /scratch/stefan/7775247/working/building/REAL300004919002 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/2 `/scratch/stefan/7775247/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCOC1=CC=CC2=CC=CC=C21)C(=O)[O-]) `REAL300004919002.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919002 none CC#CCC(NC(=O)CCCOC1=CC=CC2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 97, 73, 73, 30, 73, 20, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 97, 97, 97, 106, 106, 106, 106, 106, 97, 73, 28, 28, 24, 24, 14, 14, 1, 1, 1, 1, 1, 1, 1] 106 rigid atoms, others: [43, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 469 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919002 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919002 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919002/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919002 Building REAL300004919003 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919003' /scratch/stefan/7775247/working/building/REAL300004919003 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919003 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919003/0 /scratch/stefan/7775247/working/building/REAL300004919003 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/3 `/scratch/stefan/7775247/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCOC1=CC=C2NC(=O)CCC2=C1)C(=O)[O-]) `REAL300004919003.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919003 none CC#CCC(NC(=O)CCCOC1=CC=C2NC(=O)CCC2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 151, 151, 55, 151, 31, 11, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 183, 186, 186, 201, 201, 201, 201, 201, 183, 151, 55, 55, 31, 31, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [45, 43, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 836 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919003 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919003 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919003/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919003 Building REAL300004919004 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919004' /scratch/stefan/7775247/working/building/REAL300004919004 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919004 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919004/0 /scratch/stefan/7775247/working/building/REAL300004919004 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/4 `/scratch/stefan/7775247/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC=C2C)N=C1)C(=O)[O-]) `REAL300004919004.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919004 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC=C2C)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [134, 134, 134, 54, 13, 13, 1, 13, 1, 1, 1, 1, 1, 6, 6, 2, 6, 6, 6, 1, 1, 54, 81, 81, 134, 134, 134, 134, 134, 54, 13, 2, 2, 2, 6, 6, 2, 6, 6, 6, 6, 1] 198 rigid atoms, others: [6, 8, 9, 10, 11, 12, 19, 20, 41] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 650 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919004 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC=C2C)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [198, 198, 198, 117, 45, 45, 6, 45, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 117, 147, 147, 198, 198, 198, 198, 198, 117, 45, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6] 198 rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41]) total number of confs: 915 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919004 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919004 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919004/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919004 Building REAL300004919005 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919005' /scratch/stefan/7775247/working/building/REAL300004919005 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919005 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919005/0 /scratch/stefan/7775247/working/building/REAL300004919005 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/5 `/scratch/stefan/7775247/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C(F)(F)F)N(C2=CC=CC=C2C)N=C1)C(=O)[O-]) `REAL300004919005.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919005 none CC#CCC(NC(=O)C1=C(C(F)(F)F)N(C2=CC=CC=C2C)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 15, 15, 15, 8, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 38, 10, 10, 1, 10, 1, 1, 1, 2, 2, 2, 1, 1, 5, 5, 1, 5, 5, 5, 1, 1, 38, 60, 60, 93, 93, 93, 93, 93, 38, 10, 5, 5, 1, 5, 5, 5, 5, 1] 171 rigid atoms, others: [6, 8, 9, 10, 14, 15, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 462 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919005 none CC#CCC(NC(=O)C1=C(C(F)(F)F)N(C2=CC=CC=C2C)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 15, 15, 15, 8, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [171, 171, 171, 102, 37, 37, 5, 37, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 102, 128, 128, 171, 171, 171, 171, 171, 102, 37, 1, 1, 1, 1, 2, 2, 2, 5] 171 rigid atoms, others: [34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41]) total number of confs: 806 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919005 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919005 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919005/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919005 Building REAL300004919006 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919006' /scratch/stefan/7775247/working/building/REAL300004919006 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919006 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919006/0 /scratch/stefan/7775247/working/building/REAL300004919006 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/6 `/scratch/stefan/7775247/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC2CCCC2)C(OC)=C1)C(=O)[O-]) `REAL300004919006.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919006 none CC#CCC(NC(=O)C1=CC=C(OC2CCCC2)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 7, 20, 20, 20, 20, 1, 1, 3, 1, 13, 21, 21, 33, 33, 33, 33, 33, 13, 5, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 3, 3, 3, 1] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 46, 18, 19, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919006 none CC#CCC(NC(=O)C1=CC=C(OC2CCCC2)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 181, 181, 108, 59, 59, 20, 59, 11, 20, 20, 6, 1, 1, 1, 1, 1, 1, 20, 20, 36, 20, 108, 150, 150, 181, 181, 181, 181, 181, 108, 59, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 20] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46]) total number of confs: 965 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919006 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919006 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919006/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919006 Building REAL300004919007 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919007' /scratch/stefan/7775247/working/building/REAL300004919007 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919007 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919007/0 /scratch/stefan/7775247/working/building/REAL300004919007 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/7 `/scratch/stefan/7775247/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(CNC(=O)C2=CC=CS2)C=C1)C(=O)[O-]) `REAL300004919007.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919007 none CC#CCC(NC(=O)C1=CC=C(CNC(=O)C2=CC=CS2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 6, 33, 33, 33, 41, 41, 41, 41, 1, 1, 9, 14, 14, 27, 27, 27, 27, 27, 9, 3, 1, 1, 6, 6, 33, 41, 41, 41, 1, 1] 201 rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 12, 21, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919007 none CC#CCC(NC(=O)C1=CC=C(CNC(=O)C2=CC=CS2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 122, 64, 64, 13, 64, 13, 42, 42, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 42, 42, 122, 156, 156, 201, 201, 201, 201, 201, 122, 64, 42, 42, 12, 12, 4, 1, 1, 1, 42, 42] 201 rigid atoms, others: [38, 39, 40, 14, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42]) total number of confs: 1034 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919007 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919007 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919007/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919007 Building REAL300004919008 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919008' /scratch/stefan/7775247/working/building/REAL300004919008 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919008 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919008/0 /scratch/stefan/7775247/working/building/REAL300004919008 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/8 `/scratch/stefan/7775247/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)NC(=O)C1=CC=CC(Cl)=C1Cl)C(=O)[O-]) `REAL300004919008.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919008 none CC#CCC(NC(=O)C(C)NC(=O)C1=CC=CC(Cl)=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 16, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 73, 73, 16, 73, 7, 16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 131, 165, 165, 201, 201, 201, 201, 201, 131, 73, 16, 16, 16, 16, 7, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 11, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 967 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919008 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919008 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919008/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919008 Building REAL300004919009 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919009' /scratch/stefan/7775247/working/building/REAL300004919009 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919009 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919009/0 /scratch/stefan/7775247/working/building/REAL300004919009 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/9 `/scratch/stefan/7775247/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCN1C(=O)C1=CC(Cl)=CC=C1Cl)C(=O)[O-]) `REAL300004919009.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919009 none CC#CCC(NC(=O)C1CCCN1C(=O)C1=CC(Cl)=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 1, 1, 16, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 28, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 6, 6, 15, 15, 15, 10, 15, 15, 15, 28, 46, 46, 73, 73, 73, 73, 73, 28, 10, 1, 1, 1, 1, 1, 1, 1, 15, 10, 15] 173 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42]) total number of confs: 404 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: REAL300004919009 none CC#CCC(NC(=O)C1CCCN1C(=O)C1=CC(Cl)=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 1, 1, 16, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [173, 173, 173, 105, 53, 53, 15, 53, 15, 15, 15, 15, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 105, 139, 139, 173, 173, 173, 173, 173, 105, 53, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1] 173 rigid atoms, others: [40, 41, 42, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 860 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919009 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919009 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919009/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919009 Building REAL300004919010 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919010' /scratch/stefan/7775247/working/building/REAL300004919010 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919010 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919010/0 /scratch/stefan/7775247/working/building/REAL300004919010 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/10 `/scratch/stefan/7775247/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCN1C(=O)C1=CC(Cl)=CC=C1OC)C(=O)[O-]) `REAL300004919010.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919010 none CC#CCC(NC(=O)C1CCCN1C(=O)C1=CC(Cl)=CC=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 23, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 19, 19, 19, 33, 23, 40, 40, 68, 68, 68, 68, 68, 23, 8, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 33, 33, 33] 201 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46]) total number of confs: 392 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: REAL300004919010 none CC#CCC(NC(=O)C1CCCN1C(=O)C1=CC(Cl)=CC=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [177, 177, 177, 94, 49, 49, 19, 49, 19, 19, 19, 19, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 4, 94, 136, 136, 177, 177, 177, 177, 177, 94, 49, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 4, 4, 4] 201 rigid atoms, others: [41, 42, 43, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46]) total number of confs: 921 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919010 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919010 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919010/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919010 Building REAL300004919011 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919011' /scratch/stefan/7775247/working/building/REAL300004919011 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919011 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919011/0 /scratch/stefan/7775247/working/building/REAL300004919011 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/11 `/scratch/stefan/7775247/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCN1C(=O)C1=CC=CC=C1OC(F)F)C(=O)[O-]) `REAL300004919011.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919011 none CC#CCC(NC(=O)C1CCCN1C(=O)C1=CC=CC=C1OC(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 11, 17, 17, 17, 36, 53, 53, 15, 24, 24, 48, 48, 48, 48, 48, 15, 6, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 53] 201 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46]) 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: REAL300004919011 none CC#CCC(NC(=O)C1CCCN1C(=O)C1=CC=CC=C1OC(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [145, 145, 145, 75, 41, 41, 17, 41, 17, 17, 17, 17, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 16, 16, 75, 99, 99, 145, 145, 145, 145, 145, 75, 41, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 16] 201 rigid atoms, others: [45, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46]) total number of confs: 751 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919011 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919011 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919011/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919011 Building REAL300004919012 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919012' /scratch/stefan/7775247/working/building/REAL300004919012 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919012 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919012/0 /scratch/stefan/7775247/working/building/REAL300004919012 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/12 `/scratch/stefan/7775247/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCN(C(=O)COC2=CC=CC=C2)CC1)C(=O)[O-]) `REAL300004919012.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919012 none CC#CCC(NC(=O)C1CCN(C(=O)COC2=CC=CC=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 15, 6, 6, 1, 6, 1, 1, 1, 1, 1, 4, 4, 9, 19, 26, 26, 19, 26, 26, 1, 1, 15, 25, 25, 35, 35, 35, 35, 35, 15, 7, 1, 1, 1, 1, 1, 9, 9, 26, 26, 19, 26, 26, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 46, 47, 48, 49, 22, 23, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919012 none CC#CCC(NC(=O)C1CCN(C(=O)COC2=CC=CC=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 129, 90, 90, 26, 90, 26, 26, 26, 20, 6, 20, 4, 1, 1, 1, 1, 1, 1, 1, 26, 26, 129, 166, 166, 201, 201, 201, 201, 201, 129, 90, 26, 26, 26, 26, 26, 6, 6, 1, 1, 1, 1, 1, 26, 26, 26, 26] 201 rigid atoms, others: [41, 42, 43, 44, 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, 46, 47, 48, 49]) total number of confs: 963 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919012 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919012 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919012/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919012 Building REAL300004919013 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919013' /scratch/stefan/7775247/working/building/REAL300004919013 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919013 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919013/0 /scratch/stefan/7775247/working/building/REAL300004919013 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/13 `/scratch/stefan/7775247/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCN(C(=O)CCOC2=CC=CC=C2)CC1)C(=O)[O-]) `REAL300004919013.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919013 none CC#CCC(NC(=O)C1CCN(C(=O)CCOC2=CC=CC=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 25, 10, 10, 1, 10, 1, 1, 1, 1, 1, 6, 6, 6, 6, 13, 18, 18, 13, 18, 18, 1, 1, 25, 39, 39, 58, 58, 58, 58, 58, 25, 10, 1, 1, 1, 1, 1, 6, 6, 6, 6, 18, 18, 13, 18, 18, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 49, 50, 51, 52, 23, 24, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 321 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919013 none CC#CCC(NC(=O)C1CCN(C(=O)CCOC2=CC=CC=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 134, 84, 84, 18, 84, 18, 18, 18, 10, 6, 10, 6, 4, 1, 1, 1, 1, 1, 1, 1, 18, 18, 134, 166, 166, 201, 201, 201, 201, 201, 134, 84, 18, 18, 18, 18, 18, 6, 6, 6, 6, 1, 1, 1, 1, 1, 18, 18, 18, 18] 201 rigid atoms, others: [48, 44, 45, 46, 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, 49, 50, 51, 52]) total number of confs: 934 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919013 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919013 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919013/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919013 Building REAL300004919014 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919014' /scratch/stefan/7775247/working/building/REAL300004919014 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919014 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919014/0 /scratch/stefan/7775247/working/building/REAL300004919014 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/14 `/scratch/stefan/7775247/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CNC(=O)CC1=CC=CC(F)=C1)C(=O)[O-]) `REAL300004919014.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919014 none CC#CCC(NC(=O)CNC(=O)CC1=CC=CC(F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 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, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 127, 77, 77, 30, 81, 9, 9, 3, 9, 1, 1, 1, 1, 1, 1, 1, 1, 127, 165, 165, 201, 201, 201, 201, 201, 127, 81, 30, 30, 9, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 1064 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919014 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919014 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919014/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919014 Building REAL300004919015 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919015' /scratch/stefan/7775247/working/building/REAL300004919015 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919015 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919015/0 /scratch/stefan/7775247/working/building/REAL300004919015 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/15 `/scratch/stefan/7775247/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCN(C(=O)CCOC2=CC=CC=C2)C1)C(=O)[O-]) `REAL300004919015.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919015 none CC#CCC(NC(=O)C1CCCN(C(=O)CCOC2=CC=CC=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 28, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 6, 6, 10, 12, 22, 27, 27, 22, 27, 27, 1, 28, 44, 44, 59, 59, 59, 59, 59, 28, 11, 1, 1, 1, 1, 1, 1, 1, 10, 10, 12, 12, 27, 27, 22, 27, 27, 1, 1] 201 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 51, 52, 41, 24, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 369 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: REAL300004919015 none CC#CCC(NC(=O)C1CCCN(C(=O)CCOC2=CC=CC=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 89, 89, 27, 89, 27, 27, 27, 27, 18, 10, 18, 8, 4, 1, 1, 1, 1, 1, 1, 1, 27, 140, 171, 171, 201, 201, 201, 201, 201, 140, 89, 27, 27, 27, 27, 27, 27, 27, 10, 10, 8, 8, 1, 1, 1, 1, 1, 27, 27] 201 rigid atoms, others: [49, 50, 46, 47, 48, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 51, 52]) total number of confs: 929 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919015 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919015 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919015/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919015 Building REAL300004919016 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919016' /scratch/stefan/7775247/working/building/REAL300004919016 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919016 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919016/0 /scratch/stefan/7775247/working/building/REAL300004919016 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/16 `/scratch/stefan/7775247/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(NC(=O)CCCC2=CC=CS2)=C1)C(=O)[O-]) `REAL300004919016.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919016 none CC#CCC(NC(=O)C1=CC=CC(NC(=O)CCCC2=CC=CS2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 14, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 18, 22, 30, 44, 44, 44, 44, 1, 11, 14, 14, 19, 19, 19, 19, 19, 11, 5, 1, 1, 1, 3, 18, 18, 30, 30, 30, 30, 44, 44, 44, 1] 201 rigid atoms, others: [35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 48, 24] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 293 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919016 none CC#CCC(NC(=O)C1=CC=CC(NC(=O)CCCC2=CC=CS2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 14, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 113, 88, 88, 44, 88, 44, 44, 44, 44, 28, 28, 7, 28, 3, 3, 1, 1, 1, 1, 1, 1, 44, 113, 134, 134, 201, 201, 201, 201, 201, 113, 88, 44, 44, 44, 28, 7, 7, 3, 3, 3, 3, 1, 1, 1, 44] 201 rigid atoms, others: [45, 46, 47, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 48]) total number of confs: 938 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919016 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919016 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919016/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919016 Building REAL300004919017 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919017' /scratch/stefan/7775247/working/building/REAL300004919017 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919017 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919017/0 /scratch/stefan/7775247/working/building/REAL300004919017 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/17 `/scratch/stefan/7775247/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CC(=O)N(CC2=CC=CC(C(F)(F)F)=C2)C1)C(=O)[O-]) `REAL300004919017.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919017 none CC#CCC(NC(=O)C1CC(=O)N(CC2=CC=CC(C(F)(F)F)=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 21, 35, 35, 38, 38, 38, 38, 38, 21, 9, 1, 1, 1, 6, 6, 14, 14, 14, 14, 1, 1] 201 rigid atoms, others: [45, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 44, 24] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919017 none CC#CCC(NC(=O)C1CC(=O)N(CC2=CC=CC(C(F)(F)F)=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 129, 81, 81, 14, 81, 14, 14, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 129, 163, 163, 201, 201, 201, 201, 201, 129, 81, 14, 14, 14, 6, 6, 1, 1, 1, 1, 14, 14] 201 rigid atoms, others: [40, 41, 42, 43, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45]) total number of confs: 935 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919017 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919017 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919017/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919017 Building REAL300004919018 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919018' /scratch/stefan/7775247/working/building/REAL300004919018 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919018 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919018/0 /scratch/stefan/7775247/working/building/REAL300004919018 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/18 `/scratch/stefan/7775247/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(OC1=CC=CC=C1)C1=CC=CC=C1)C(=O)[O-]) `REAL300004919018.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919018 none CC#CCC(NC(=O)C(OC1=CC=CC=C1)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 184, 184, 103, 61, 61, 12, 61, 5, 1, 1, 1, 1, 1, 1, 1, 12, 23, 23, 14, 23, 23, 103, 140, 140, 184, 184, 184, 184, 184, 103, 61, 12, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23] 201 rigid atoms, others: [33, 34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42]) total number of confs: 964 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919018 none CC#CCC(NC(=O)C(OC1=CC=CC=C1)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 45, 20, 20, 4, 20, 1, 4, 11, 23, 23, 11, 23, 23, 1, 1, 1, 1, 1, 1, 45, 69, 69, 103, 103, 103, 103, 103, 45, 20, 4, 23, 23, 11, 23, 23, 1, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 8, 41, 42, 16, 17, 18, 19, 20, 21, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 580 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919018 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919018 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919018/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919018 Building REAL300004919019 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919019' /scratch/stefan/7775247/working/building/REAL300004919019 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919019 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919019/0 /scratch/stefan/7775247/working/building/REAL300004919019 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/19 `/scratch/stefan/7775247/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1S(=O)(=O)N1CCOCC1)C(=O)[O-]) `REAL300004919019.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919019 none CC#CCC(NC(=O)C1=CC=CC=C1S(=O)(=O)N1CCOCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 2, 2, 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: [34, 34, 34, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 13, 22, 22, 34, 34, 34, 34, 34, 13, 5, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11] 71 rigid atoms, others: [33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 196 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: REAL300004919019 none CC#CCC(NC(=O)C1=CC=CC=C1S(=O)(=O)N1CCOCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 40, 20, 20, 11, 20, 11, 11, 9, 11, 11, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 40, 56, 56, 71, 71, 71, 71, 71, 40, 20, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1] 71 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 14, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 392 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919019 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919019 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919019/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919019 Building REAL300004919020 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919020' /scratch/stefan/7775247/working/building/REAL300004919020 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919020 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919020/0 /scratch/stefan/7775247/working/building/REAL300004919020 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/20 `/scratch/stefan/7775247/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=CC(Br)=CC=C2N1)C(=O)[O-]) `REAL300004919020.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919020 none CC#CCC(NC(=O)C1=CC2=CC(Br)=CC=C2N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 35, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 43, 43, 65, 65, 65, 65, 65, 35, 11, 1, 1, 1, 1, 1] 65 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919020 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919020 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919020/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919020 Building REAL300004919021 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919021' /scratch/stefan/7775247/working/building/REAL300004919021 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919021 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919021/0 /scratch/stefan/7775247/working/building/REAL300004919021 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/21 `/scratch/stefan/7775247/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(OCC2=CC=CS2)=C1)C(=O)[O-]) `REAL300004919021.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919021 none CC#CCC(NC(=O)C1=CC=CC(OCC2=CC=CS2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 14, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 16, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 3, 3, 9, 9, 9, 9, 1, 16, 22, 22, 43, 43, 43, 43, 43, 16, 5, 1, 1, 1, 3, 3, 9, 9, 9, 1] 201 rigid atoms, others: [32, 33, 6, 39, 8, 9, 10, 11, 12, 13, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919021 none CC#CCC(NC(=O)C1=CC=CC(OCC2=CC=CS2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 14, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 87, 30, 30, 9, 30, 9, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 9, 87, 121, 121, 201, 201, 201, 201, 201, 87, 30, 9, 9, 9, 5, 5, 1, 1, 1, 9] 201 rigid atoms, others: [36, 37, 38, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39]) total number of confs: 957 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919021 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919021 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919021/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919021 Building REAL300004919022 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919022' /scratch/stefan/7775247/working/building/REAL300004919022 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919022 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919022/0 /scratch/stefan/7775247/working/building/REAL300004919022 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/22 `/scratch/stefan/7775247/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Cl)=C(Cl)N1C)C(=O)[O-]) `REAL300004919022.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919022 none CC#CCC(NC(=O)C1=CC(Cl)=C(Cl)N1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'Cl', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 16, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 39, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 39, 54, 54, 72, 72, 72, 72, 72, 39, 13, 1, 2, 2, 2] 72 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 26] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29]) total number of confs: 363 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919022 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919022 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919022/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919022 Building REAL300004919023 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919023' /scratch/stefan/7775247/working/building/REAL300004919023 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919023 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919023/0 /scratch/stefan/7775247/working/building/REAL300004919023 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/23 `/scratch/stefan/7775247/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCN(C2=CC=CC=C2Br)C1=O)C(=O)[O-]) `REAL300004919023.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919023 none CC#CCC(NC(=O)C1CCN(C2=CC=CC=C2Br)C1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 17, 1, 11, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 33, 11, 11, 1, 11, 1, 1, 1, 1, 1, 6, 6, 2, 6, 6, 6, 1, 1, 33, 52, 52, 86, 86, 86, 86, 86, 33, 11, 1, 1, 1, 1, 1, 6, 6, 2, 6] 201 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39]) total number of confs: 428 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919023 none CC#CCC(NC(=O)C1CCN(C2=CC=CC=C2Br)C1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 17, 1, 11, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 123, 54, 54, 6, 54, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 123, 147, 147, 201, 201, 201, 201, 201, 123, 54, 6, 6, 6, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 922 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919023 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919023 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919023/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919023 Building REAL300004919024 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919024' /scratch/stefan/7775247/working/building/REAL300004919024 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919024 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919024/0 /scratch/stefan/7775247/working/building/REAL300004919024 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/24 `/scratch/stefan/7775247/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCN1CCCS1(=O)=O)C(=O)[O-]) `REAL300004919024.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919024 none CC#CCC(NC(=O)CCN1CCCS1(=O)=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 8, 5, 5, 5, 14, 11, 11, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 130, 78, 78, 15, 78, 13, 1, 1, 1, 1, 1, 1, 1, 1, 143, 166, 166, 201, 201, 201, 201, 198, 143, 78, 15, 15, 13, 13, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 954 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919024 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919024 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919024/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919024 Building REAL300004919025 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919025' /scratch/stefan/7775247/working/building/REAL300004919025 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919025 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919025/0 /scratch/stefan/7775247/working/building/REAL300004919025 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/25 `/scratch/stefan/7775247/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(OCCC)C=C1)C(=O)[O-]) `REAL300004919025.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919025 none CC#CCC(NC(=O)C=CC1=CC=C(OCCC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 29, 13, 13, 3, 13, 3, 1, 1, 1, 1, 1, 1, 7, 17, 28, 1, 1, 29, 53, 53, 52, 52, 52, 52, 52, 29, 13, 3, 3, 1, 1, 17, 17, 28, 28, 28, 28, 28, 1, 1] 201 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 18, 19, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 437 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919025 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919025 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919025/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919025 Building REAL300004919026 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919026' /scratch/stefan/7775247/working/building/REAL300004919026 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919026 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919026/0 /scratch/stefan/7775247/working/building/REAL300004919026 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/26 `/scratch/stefan/7775247/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCC1=NC(C2=CC=CS2)=NO1)C(=O)[O-]) `REAL300004919026.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919026 none CC#CCC(NC(=O)CCCC1=NC(C2=CC=CS2)=NO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'O.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 14, 8, 12, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [141, 141, 141, 134, 93, 93, 32, 93, 16, 8, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1, 134, 137, 137, 141, 141, 141, 141, 141, 134, 93, 31, 31, 16, 16, 8, 8, 4, 4, 4] 201 rigid atoms, others: [10, 11, 12, 13, 14, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 616 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919026 none CC#CCC(NC(=O)CCCC1=NC(C2=CC=CS2)=NO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'O.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 14, 8, 12, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 143, 143, 56, 143, 34, 18, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 194, 197, 197, 201, 201, 201, 201, 201, 194, 143, 56, 56, 34, 34, 18, 18, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 875 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919026 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919026 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919026/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919026 Building REAL300004919027 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919027' /scratch/stefan/7775247/working/building/REAL300004919027 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919027 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919027/0 /scratch/stefan/7775247/working/building/REAL300004919027 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/27 `/scratch/stefan/7775247/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(C2=CSC(C)=N2)=C1)C(=O)[O-]) `REAL300004919027.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919027 none CC#CCC(NC(=O)C1=CC=CC(C2=CSC(C)=N2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 14, 1, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 16, 26, 26, 39, 39, 39, 39, 39, 16, 5, 1, 1, 1, 13, 13, 13, 13, 1] 201 rigid atoms, others: [32, 37, 6, 8, 9, 10, 11, 12, 13, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36]) 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: REAL300004919027 none CC#CCC(NC(=O)C1=CC=CC(C2=CSC(C)=N2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 14, 1, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 49, 49, 13, 49, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 116, 145, 145, 201, 201, 201, 201, 201, 116, 49, 13, 13, 13, 1, 2, 2, 2, 13] 201 rigid atoms, others: [33, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37]) total number of confs: 928 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919027 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919027 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919027/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919027 Building REAL300004919028 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919028' /scratch/stefan/7775247/working/building/REAL300004919028 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919028 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919028/0 /scratch/stefan/7775247/working/building/REAL300004919028 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/28 `/scratch/stefan/7775247/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CS(=O)(=O)CCCC1=CC=CC=C1)C(=O)[O-]) `REAL300004919028.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919028 none CC#CCC(NC(=O)CS(=O)(=O)CCCC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 14, 11, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 97, 89, 64, 64, 36, 64, 14, 6, 14, 14, 4, 2, 1, 1, 1, 1, 1, 1, 1, 89, 89, 89, 97, 97, 97, 97, 97, 89, 64, 36, 36, 6, 6, 4, 4, 2, 2, 1, 1, 1, 1, 1] 97 rigid atoms, others: [39, 40, 41, 42, 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]) total number of confs: 438 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919028 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919028 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919028/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919028 Building REAL300004919029 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919029' /scratch/stefan/7775247/working/building/REAL300004919029 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919029 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919029/0 /scratch/stefan/7775247/working/building/REAL300004919029 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/29 `/scratch/stefan/7775247/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CS(=O)(=O)C1CCCC1)C(=O)[O-]) `REAL300004919029.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919029 none CC#CCC(NC(=O)CS(=O)(=O)C1CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 14, 11, 11, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 117, 60, 60, 20, 60, 6, 1, 6, 6, 1, 1, 1, 1, 1, 117, 154, 154, 201, 201, 201, 201, 201, 117, 60, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 9, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 988 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919029 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919029 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919029/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919029 Building REAL300004919030 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919030' /scratch/stefan/7775247/working/building/REAL300004919030 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919030 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919030/0 /scratch/stefan/7775247/working/building/REAL300004919030 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/30 `/scratch/stefan/7775247/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1S(=O)(=O)CCC)C(=O)[O-]) `REAL300004919030.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919030 none CC#CCC(NC(=O)C1=CC=CC=C1S(=O)(=O)CCC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 20, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 14, 20, 32, 32, 60, 60, 60, 60, 60, 20, 7, 1, 1, 1, 1, 12, 12, 14, 14, 14, 14, 14] 113 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 333 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919030 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919030 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919030/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919030 Building REAL300004919031 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919031' /scratch/stefan/7775247/working/building/REAL300004919031 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919031 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919031/0 /scratch/stefan/7775247/working/building/REAL300004919031 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/31 `/scratch/stefan/7775247/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1S(=O)(=O)C(C)C)C(=O)[O-]) `REAL300004919031.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919031 none CC#CCC(NC(=O)C1=CC=CC=C1S(=O)(=O)C(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 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: [49, 49, 49, 20, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 20, 32, 32, 49, 49, 49, 49, 49, 20, 7, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7] 59 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 270 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919031 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919031 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919031/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919031 Building REAL300004919032 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919032' /scratch/stefan/7775247/working/building/REAL300004919032 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919032 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919032/0 /scratch/stefan/7775247/working/building/REAL300004919032 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/32 `/scratch/stefan/7775247/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CSCN1C(=O)CCC)C(=O)[O-]) `REAL300004919032.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919032 none CC#CCC(NC(=O)C1CSCN1C(=O)CCC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 5, 14, 5, 8, 1, 11, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 25, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 4, 4, 23, 28, 25, 41, 41, 70, 70, 70, 70, 70, 25, 8, 1, 1, 1, 1, 1, 23, 23, 32, 32, 33, 33, 33] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 487 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919032 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919032 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919032/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919032 Building REAL300004919033 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919033' /scratch/stefan/7775247/working/building/REAL300004919033 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919033 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919033/0 /scratch/stefan/7775247/working/building/REAL300004919033 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/33 `/scratch/stefan/7775247/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CSCN1C(=O)CC(C)(C)C)C(=O)[O-]) `REAL300004919033.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919033 none CC#CCC(NC(=O)C1CSCN1C(=O)CC(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 14, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 22, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 4, 4, 9, 12, 12, 12, 22, 35, 35, 54, 54, 54, 54, 54, 22, 9, 1, 1, 1, 1, 1, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12] 80 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 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]) total number of confs: 319 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919033 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919033 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919033/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919033 Building REAL300004919034 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919034' /scratch/stefan/7775247/working/building/REAL300004919034 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919034 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919034/0 /scratch/stefan/7775247/working/building/REAL300004919034 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/34 `/scratch/stefan/7775247/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CSCN1C(=O)CCCC)C(=O)[O-]) `REAL300004919034.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919034 none CC#CCC(NC(=O)C1CSCN1C(=O)CCCC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 14, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 21, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 4, 4, 22, 28, 36, 21, 37, 37, 58, 58, 58, 58, 58, 21, 8, 1, 1, 1, 1, 1, 22, 22, 31, 31, 36, 36, 37, 37, 37] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 468 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919034 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919034 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919034/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919034 Building REAL300004919035 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919035' /scratch/stefan/7775247/working/building/REAL300004919035 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919035 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919035/0 /scratch/stefan/7775247/working/building/REAL300004919035 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/35 `/scratch/stefan/7775247/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCN1C(=O)C1=CC=C2OCOC2=C1)C(=O)[O-]) `REAL300004919035.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919035 none CC#CCC(NC(=O)C1CCCN1C(=O)C1=CC=C2OCOC2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 2, 2, 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: [41, 41, 41, 21, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 19, 19, 19, 19, 19, 19, 19, 19, 21, 28, 28, 41, 41, 41, 41, 41, 21, 8, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19] 102 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45]) total number of confs: 223 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: REAL300004919035 none CC#CCC(NC(=O)C1CCCN1C(=O)C1=CC=C2OCOC2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 2, 2, 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: [102, 102, 102, 69, 43, 43, 19, 43, 19, 19, 19, 19, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 69, 82, 82, 102, 102, 102, 102, 102, 69, 43, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1] 102 rigid atoms, others: [45, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 459 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919035 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919035 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919035/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919035 Building REAL300004919036 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919036' /scratch/stefan/7775247/working/building/REAL300004919036 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919036 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919036/0 /scratch/stefan/7775247/working/building/REAL300004919036 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/36 `/scratch/stefan/7775247/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Cl)=C(N2C=CC=C2)C=C1OC)C(=O)[O-]) `REAL300004919036.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919036 none CC#CCC(NC(=O)C1=CC(Cl)=C(N2C=CC=C2)C=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 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: [121, 121, 121, 49, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1, 1, 4, 49, 77, 77, 121, 121, 121, 121, 121, 49, 12, 1, 4, 4, 4, 4, 1, 3, 4, 4] 197 rigid atoms, others: [32, 37, 6, 8, 9, 10, 11, 12, 13, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 584 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919036 none CC#CCC(NC(=O)C1=CC(Cl)=C(N2C=CC=C2)C=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 16, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 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: [178, 178, 178, 73, 25, 25, 3, 25, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 73, 119, 119, 178, 178, 178, 178, 178, 73, 25, 3, 1, 1, 1, 1, 3, 7, 7, 7] 194 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40]) total number of confs: 902 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919036 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919036 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919036/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919036 Building REAL300004919037 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919037' /scratch/stefan/7775247/working/building/REAL300004919037 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919037 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919037/0 /scratch/stefan/7775247/working/building/REAL300004919037 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/37 `/scratch/stefan/7775247/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CSCN1C(=O)C1=CC=C(OCC)C=C1)C(=O)[O-]) `REAL300004919037.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919037 none CC#CCC(NC(=O)C1CSCN1C(=O)C1=CC=C(OCC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 14, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 26, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 6, 6, 10, 10, 7, 7, 30, 45, 10, 10, 26, 40, 40, 54, 54, 54, 54, 54, 26, 8, 1, 1, 1, 1, 1, 10, 10, 45, 45, 45, 45, 45, 10, 10] 161 rigid atoms, others: [34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 408 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919037 none CC#CCC(NC(=O)C1CSCN1C(=O)C1=CC=C(OCC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 14, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 54, 26, 26, 10, 26, 10, 10, 10, 10, 4, 1, 4, 1, 1, 1, 1, 1, 6, 13, 1, 1, 54, 73, 73, 91, 91, 91, 91, 91, 54, 26, 10, 10, 10, 10, 10, 1, 1, 13, 13, 13, 13, 13, 1, 1] 161 rigid atoms, others: [39, 40, 13, 46, 15, 16, 17, 18, 19, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 475 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919037 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919037 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919037/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919037 Building REAL300004919038 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919038' /scratch/stefan/7775247/working/building/REAL300004919038 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919038 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919038/0 /scratch/stefan/7775247/working/building/REAL300004919038 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/38 `/scratch/stefan/7775247/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CSCN1C(=O)C1=CC=C(Cl)C=C1)C(=O)[O-]) `REAL300004919038.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919038 none CC#CCC(NC(=O)C1CSCN1C(=O)C1=CC=C(Cl)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 14, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [34, 34, 34, 18, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 10, 10, 5, 6, 10, 10, 18, 26, 26, 34, 34, 34, 34, 34, 18, 8, 1, 1, 1, 1, 1, 10, 10, 10, 10] 49 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40]) total number of confs: 206 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: REAL300004919038 none CC#CCC(NC(=O)C1CSCN1C(=O)C1=CC=C(Cl)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 14, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 34, 20, 20, 10, 20, 10, 10, 10, 10, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 34, 41, 41, 49, 49, 49, 49, 49, 34, 20, 10, 10, 10, 10, 10, 1, 1, 1, 1] 49 rigid atoms, others: [37, 38, 39, 40, 13, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 226 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919038 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919038 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919038/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919038 Building REAL300004919039 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919039' /scratch/stefan/7775247/working/building/REAL300004919039 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919039 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919039/0 /scratch/stefan/7775247/working/building/REAL300004919039 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/39 `/scratch/stefan/7775247/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=CC=C1OC(C)C)C(=O)[O-]) `REAL300004919039.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919039 none CC#CCC(NC(=O)CC1=CC=CC=C1OC(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [135, 135, 135, 64, 34, 34, 6, 34, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 64, 93, 93, 135, 135, 135, 135, 135, 64, 34, 6, 6, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 698 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919039 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919039 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919039/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919039 Building REAL300004919040 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919040' /scratch/stefan/7775247/working/building/REAL300004919040 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919040 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919040/0 /scratch/stefan/7775247/working/building/REAL300004919040 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/40 `/scratch/stefan/7775247/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCOC1=CC=CC=C1Br)C(=O)[O-]) `REAL300004919040.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919040 none CC#CCC(NC(=O)CCCOC1=CC=CC=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 17, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 130, 100, 100, 45, 100, 38, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 130, 158, 158, 201, 201, 201, 201, 201, 130, 100, 45, 45, 38, 38, 25, 25, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 1013 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919040 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919040 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919040/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919040 Building REAL300004919041 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919041' /scratch/stefan/7775247/working/building/REAL300004919041 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919041 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919041/0 /scratch/stefan/7775247/working/building/REAL300004919041 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/41 `/scratch/stefan/7775247/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CNC(=O)NCC1=CC=C(Cl)C=C1)C(=O)[O-]) `REAL300004919041.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919041 none CC#CCC(NC(=O)CNC(=O)NCC1=CC=C(Cl)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 8, 1, 11, 8, 5, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 117, 117, 40, 119, 14, 14, 13, 14, 3, 1, 1, 1, 1, 1, 1, 1, 1, 175, 179, 179, 201, 201, 201, 201, 201, 175, 119, 40, 40, 14, 13, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 835 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919041 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919041 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919041/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919041 Building REAL300004919042 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919042' /scratch/stefan/7775247/working/building/REAL300004919042 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919042 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919042/0 /scratch/stefan/7775247/working/building/REAL300004919042 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/42 `/scratch/stefan/7775247/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)OC1=CC=CC=C1C(F)(F)F)C(=O)[O-]) `REAL300004919042.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919042 none CC#CCC(NC(=O)C(C)OC1=CC=CC=C1C(F)(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 99, 58, 58, 14, 58, 6, 14, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 99, 144, 144, 201, 201, 201, 201, 201, 99, 58, 14, 14, 14, 14, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 1035 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919042 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919042 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919042/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919042 Building REAL300004919043 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919043' /scratch/stefan/7775247/working/building/REAL300004919043 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919043 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919043/0 /scratch/stefan/7775247/working/building/REAL300004919043 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/43 `/scratch/stefan/7775247/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)OC1=CC(Cl)=CC(Cl)=C1)C(=O)[O-]) `REAL300004919043.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919043 none CC#CCC(NC(=O)C(C)OC1=CC(Cl)=CC(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 117, 67, 67, 14, 67, 6, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 117, 158, 158, 201, 201, 201, 201, 201, 117, 67, 14, 14, 14, 14, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 1022 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919043 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919043 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919043/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919043 Building REAL300004919044 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919044' /scratch/stefan/7775247/working/building/REAL300004919044 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919044 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919044/0 /scratch/stefan/7775247/working/building/REAL300004919044 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/44 `/scratch/stefan/7775247/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCCCC1=CC=C(OC)C=C1)C(=O)[O-]) `REAL300004919044.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919044 none CC#CCC(NC(=O)CCCCCC1=CC=C(OC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 82, 82, 17, 82, 8, 6, 4, 2, 1, 1, 1, 1, 1, 1, 2, 1, 1, 117, 117, 117, 201, 201, 201, 201, 200, 117, 82, 17, 17, 8, 8, 6, 6, 4, 4, 2, 2, 1, 1, 3, 3, 3, 1, 1] 201 rigid atoms, others: [41, 42, 12, 13, 14, 15, 16, 17, 19, 20, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 855 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919044 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919044 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919044/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919044 Building REAL300004919045 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919045' /scratch/stefan/7775247/working/building/REAL300004919045 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919045 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919045/0 /scratch/stefan/7775247/working/building/REAL300004919045 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/45 `/scratch/stefan/7775247/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C(C)C)S(=O)(=O)C1CCCCC1)C(=O)[O-]) `REAL300004919045.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919045 none CC#CCC(NC(=O)C(C(C)C)S(=O)(=O)C1CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 14, 11, 11, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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, 7, 6, 6, 3, 6, 3, 3, 5, 5, 1, 3, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 9, 9, 9, 9, 9, 7, 6, 3, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 9 rigid atoms, others: [48, 49, 39, 40, 41, 42, 43, 12, 45, 46, 15, 16, 17, 18, 19, 20, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919045 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919045 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919045/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919045 Building REAL300004919046 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919046' /scratch/stefan/7775247/working/building/REAL300004919046 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919046 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919046/0 /scratch/stefan/7775247/working/building/REAL300004919046 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/46 `/scratch/stefan/7775247/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(NC(C)=O)=CC=C1[N-]S(C)(=O)=O)C(=O)[O-]) `REAL300004919046.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919046 none CC#CCC(NC(=O)C1=CC(NC(C)=O)=CC=C1[N-]S(C)(=O)=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 8, 1, 5, 11, 1, 1, 1, 8, 14, 5, 11, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 2, 2, 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, 7, 7, 4, 3, 3, 1, 3, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 2, 3, 3, 3, 4, 4, 4, 7, 7, 7, 7, 7, 4, 3, 1, 3, 3, 3, 3, 1, 1, 3, 3, 3] 10 rigid atoms, others: [33, 38, 6, 39, 8, 9, 10, 11, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919046 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919046 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919046/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919046 Building REAL300004919047 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919047' /scratch/stefan/7775247/working/building/REAL300004919047 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919047 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919047/0 /scratch/stefan/7775247/working/building/REAL300004919047 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/47 `/scratch/stefan/7775247/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=C(C)OC(C2=CSC=C2)=N1)C(=O)[O-]) `REAL300004919047.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919047 none CC#CCC(NC(=O)CC1=C(C)OC(C2=CSC=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 5, 12, 1, 1, 1, 14, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 111, 56, 29, 28, 6, 29, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 56, 83, 83, 111, 111, 111, 111, 111, 56, 28, 6, 6, 2, 2, 2, 5, 5, 5] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 595 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919047 none CC#CCC(NC(=O)CC1=C(C)OC(C2=CSC=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 5, 12, 1, 1, 1, 14, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 111, 59, 59, 15, 59, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 111, 159, 159, 201, 201, 201, 201, 201, 111, 59, 15, 15, 5, 5, 5, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 1054 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919047 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919047 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919047/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919047 Building REAL300004919048 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919048' /scratch/stefan/7775247/working/building/REAL300004919048 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919048 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919048/0 /scratch/stefan/7775247/working/building/REAL300004919048 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/48 `/scratch/stefan/7775247/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C1=CC=CC=C1)N1CCCCC1=O)C(=O)[O-]) `REAL300004919048.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919048 none CC#CCC(NC(=O)C(C1=CC=CC=C1)N1CCCCC1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 11, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 19, 7, 7, 3, 7, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 19, 26, 26, 39, 39, 39, 39, 39, 19, 7, 3, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5] 40 rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 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]) 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: REAL300004919048 none CC#CCC(NC(=O)C(C1=CC=CC=C1)N1CCCCC1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 11, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 21, 10, 10, 4, 10, 1, 4, 5, 5, 4, 5, 5, 1, 1, 1, 1, 1, 1, 1, 21, 28, 28, 40, 40, 40, 40, 40, 21, 10, 4, 5, 5, 4, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1] 40 rigid atoms, others: [38, 39, 8, 41, 42, 43, 44, 45, 15, 16, 17, 18, 19, 20, 21, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 203 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919048 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919048 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919048/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919048 Building REAL300004919049 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919049' /scratch/stefan/7775247/working/building/REAL300004919049 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919049 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919049/0 /scratch/stefan/7775247/working/building/REAL300004919049 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/49 `/scratch/stefan/7775247/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C1=CC=CC=C1)N1CCS(=O)(=O)CC1)C(=O)[O-]) `REAL300004919049.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919049 none CC#CCC(NC(=O)C(C1=CC=CC=C1)N1CCS(=O)(=O)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 10, 5, 5, 14, 11, 11, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 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: [73, 73, 73, 35, 14, 14, 4, 14, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 8, 8, 8, 8, 35, 52, 52, 73, 73, 73, 73, 73, 35, 14, 4, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8] 75 rigid atoms, others: [34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 383 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919049 none CC#CCC(NC(=O)C(C1=CC=CC=C1)N1CCS(=O)(=O)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 10, 5, 5, 14, 11, 11, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 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: [74, 74, 74, 37, 18, 18, 7, 18, 1, 7, 8, 8, 7, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 37, 51, 51, 74, 74, 74, 74, 74, 37, 18, 7, 8, 8, 7, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1] 75 rigid atoms, others: [39, 8, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 373 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919049 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919049 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919049/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919049 Building REAL300004919050 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919050' /scratch/stefan/7775247/working/building/REAL300004919050 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919050 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919050/0 /scratch/stefan/7775247/working/building/REAL300004919050 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/50 `/scratch/stefan/7775247/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(NC(=O)CC(C)C)C1=CC=CC=C1)C(=O)[O-]) `REAL300004919050.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919050 none CC#CCC(NC(=O)C(NC(=O)CC(C)C)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 39, 17, 17, 4, 17, 1, 4, 5, 5, 5, 18, 18, 21, 1, 1, 1, 1, 1, 1, 39, 57, 57, 85, 85, 85, 85, 85, 39, 17, 4, 5, 18, 18, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1] 201 rigid atoms, others: [8, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 506 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919050 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919050 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919050/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919050 Building REAL300004919051 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919051' /scratch/stefan/7775247/working/building/REAL300004919051 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919051 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919051/0 /scratch/stefan/7775247/working/building/REAL300004919051 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/51 `/scratch/stefan/7775247/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)(C)C1=CC=CC(C(F)(F)F)=C1)C(=O)[O-]) `REAL300004919051.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919051 none CC#CCC(NC(=O)C(C)(C)C1=CC=CC(C(F)(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 101, 52, 52, 13, 52, 1, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 101, 146, 146, 201, 201, 201, 201, 201, 101, 52, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 1030 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919051 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919051 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919051/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919051 Building REAL300004919052 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919052' /scratch/stefan/7775247/working/building/REAL300004919052 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919052 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919052/0 /scratch/stefan/7775247/working/building/REAL300004919052 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/52 `/scratch/stefan/7775247/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC=CC(OC2CCCC2)=C1)C(=O)[O-]) `REAL300004919052.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919052 none CC#CCC(NC(=O)CCC1=CC=CC(OC2CCCC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 23, 23, 6, 23, 2, 1, 1, 1, 1, 1, 1, 1, 11, 30, 30, 30, 30, 1, 43, 48, 48, 64, 64, 64, 64, 64, 43, 24, 6, 6, 2, 2, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1] 201 rigid atoms, others: [36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 48, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 363 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919052 none CC#CCC(NC(=O)CCC1=CC=CC(OC2CCCC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 152, 152, 86, 152, 51, 30, 30, 13, 30, 30, 6, 1, 1, 1, 1, 1, 1, 30, 179, 187, 187, 201, 201, 201, 201, 201, 179, 152, 86, 86, 51, 51, 13, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30] 201 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48]) total number of confs: 873 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919052 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919052 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919052/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919052 Building REAL300004919053 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919053' /scratch/stefan/7775247/working/building/REAL300004919053 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919053 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919053/0 /scratch/stefan/7775247/working/building/REAL300004919053 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/53 `/scratch/stefan/7775247/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=CC(OC(C)C)=C1)C(=O)[O-]) `REAL300004919053.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919053 none CC#CCC(NC(=O)C=CC1=CC=CC(OC(C)C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 35, 19, 19, 5, 19, 5, 1, 1, 1, 1, 1, 1, 1, 7, 14, 14, 1, 35, 56, 56, 73, 73, 73, 73, 73, 35, 19, 5, 5, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 1] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 19, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 432 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919053 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919053 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919053/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919053 Building REAL300004919054 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919054' /scratch/stefan/7775247/working/building/REAL300004919054 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919054 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919054/0 /scratch/stefan/7775247/working/building/REAL300004919054 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/54 `/scratch/stefan/7775247/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCC1=CC=C(C(C)(C)C)C=C1)C(=O)[O-]) `REAL300004919054.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919054 none CC#CCC(NC(=O)CCCC1=CC=C(C(C)(C)C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [148, 148, 148, 64, 28, 28, 6, 28, 4, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 64, 106, 106, 148, 148, 148, 148, 148, 64, 28, 6, 6, 4, 4, 2, 2, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1] 201 rigid atoms, others: [37, 38, 10, 11, 12, 13, 14, 15, 48, 49, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 793 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919054 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919054 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919054/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919054 Building REAL300004919055 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919055' /scratch/stefan/7775247/working/building/REAL300004919055 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919055 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919055/0 /scratch/stefan/7775247/working/building/REAL300004919055 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/55 `/scratch/stefan/7775247/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=C(S(N)(=O)=O)C=C1)C(=O)[O-]) `REAL300004919055.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919055 none CC#CCC(NC(=O)CC1=CC=C(S(N)(=O)=O)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 9, 9, 4, 9, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 32, 46, 46, 79, 79, 79, 79, 79, 32, 9, 4, 4, 1, 1, 5, 5, 1, 1] 201 rigid atoms, others: [32, 35, 36, 8, 9, 10, 11, 12, 13, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 389 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919055 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919055 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919055/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919055 Building REAL300004919056 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919056' /scratch/stefan/7775247/working/building/REAL300004919056 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919056 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919056/0 /scratch/stefan/7775247/working/building/REAL300004919056 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/56 `/scratch/stefan/7775247/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CSC(C2=CC=CC=C2Cl)=N1)C(=O)[O-]) `REAL300004919056.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919056 none CC#CCC(NC(=O)C1=CSC(C2=CC=CC=C2Cl)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 16, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 31, 9, 10, 1, 10, 1, 1, 1, 1, 1, 11, 11, 1, 11, 11, 11, 1, 31, 48, 48, 75, 75, 75, 75, 75, 31, 10, 1, 11, 11, 1, 11] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 389 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919056 none CC#CCC(NC(=O)C1=CSC(C2=CC=CC=C2Cl)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 16, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 121, 53, 53, 11, 53, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 121, 156, 156, 201, 201, 201, 201, 201, 121, 53, 11, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 960 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919056 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919056 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919056/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919056 Building REAL300004919057 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919057' /scratch/stefan/7775247/working/building/REAL300004919057 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919057 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919057/0 /scratch/stefan/7775247/working/building/REAL300004919057 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/57 `/scratch/stefan/7775247/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=CC(C(F)(F)F)=C2)CC1)C(=O)[O-]) `REAL300004919057.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919057 none CC#CCC(NC(=O)C1(C2=CC=CC(C(F)(F)F)=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 33, 13, 13, 1, 13, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 1, 1, 33, 53, 53, 87, 87, 87, 87, 87, 33, 13, 7, 7, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 6, 8, 9, 19, 20, 38] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 437 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: REAL300004919057 none CC#CCC(NC(=O)C1(C2=CC=CC(C(F)(F)F)=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 94, 46, 46, 7, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 94, 139, 139, 201, 201, 201, 201, 201, 94, 46, 1, 1, 1, 1, 7, 7, 7, 7] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 1008 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919057 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919057 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919057/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919057 Building REAL300004919058 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919058' /scratch/stefan/7775247/working/building/REAL300004919058 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919058 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919058/0 /scratch/stefan/7775247/working/building/REAL300004919058 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/58 `/scratch/stefan/7775247/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(CNC(=O)C2CCCC2)C=C1)C(=O)[O-]) `REAL300004919058.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919058 none CC#CCC(NC(=O)C1=CC=C(CNC(=O)C2CCCC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 6, 20, 20, 20, 57, 57, 57, 57, 1, 1, 7, 11, 11, 17, 17, 17, 17, 17, 7, 3, 1, 1, 6, 6, 20, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1] 201 rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 12, 47, 48, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) 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: REAL300004919058 none CC#CCC(NC(=O)C1=CC=C(CNC(=O)C2CCCC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 127, 86, 86, 26, 86, 26, 57, 57, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 57, 57, 127, 156, 156, 201, 201, 201, 201, 201, 127, 86, 57, 57, 26, 26, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57] 201 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 1032 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919058 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919058 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919058/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919058 Building REAL300004919059 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919059' /scratch/stefan/7775247/working/building/REAL300004919059 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919059 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919059/0 /scratch/stefan/7775247/working/building/REAL300004919059 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/59 `/scratch/stefan/7775247/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC(NC(C)=O)C1=C(F)C=CC=C1F)C(=O)[O-]) `REAL300004919059.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919059 none CC#CCC(NC(=O)CC(NC(C)=O)C1=C(F)C=CC=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 8, 1, 5, 11, 1, 1, 15, 1, 1, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 165, 165, 85, 46, 46, 12, 46, 5, 1, 5, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 85, 123, 123, 165, 165, 165, 165, 165, 85, 46, 12, 12, 5, 7, 7, 7, 7, 1, 1, 1] 201 rigid atoms, others: [39, 40, 9, 14, 15, 16, 17, 18, 19, 20, 21, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 823 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919059 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919059 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919059/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919059 Building REAL300004919060 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919060' /scratch/stefan/7775247/working/building/REAL300004919060 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919060 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919060/0 /scratch/stefan/7775247/working/building/REAL300004919060 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/60 `/scratch/stefan/7775247/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CSC(C2=CC=C(Br)S2)=N1)C(=O)[O-]) `REAL300004919060.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919060 none CC#CCC(NC(=O)C1=CSC(C2=CC=C(Br)S2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 17, 14, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [90, 90, 90, 35, 11, 11, 1, 11, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 35, 54, 54, 90, 90, 90, 90, 90, 35, 11, 1, 13, 13] 178 rigid atoms, others: [6, 8, 9, 10, 11, 12, 18, 29] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 436 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919060 none CC#CCC(NC(=O)C1=CSC(C2=CC=C(Br)S2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 17, 14, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [178, 178, 178, 114, 57, 57, 13, 57, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 114, 139, 139, 178, 178, 178, 178, 178, 114, 57, 13, 1, 1] 178 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 821 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919060 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919060 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919060/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919060 Building REAL300004919061 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919061' /scratch/stefan/7775247/working/building/REAL300004919061 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919061 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919061/0 /scratch/stefan/7775247/working/building/REAL300004919061 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/61 `/scratch/stefan/7775247/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CSC(C2=CC=CC=C2C)=N1)C(=O)[O-]) `REAL300004919061.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919061 none CC#CCC(NC(=O)C1=CSC(C2=CC=CC=C2C)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 29, 10, 10, 1, 10, 1, 1, 1, 1, 1, 10, 10, 1, 10, 10, 10, 1, 29, 47, 47, 74, 74, 74, 74, 74, 29, 10, 1, 10, 10, 1, 10, 10, 10, 10] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 369 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919061 none CC#CCC(NC(=O)C1=CSC(C2=CC=CC=C2C)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 129, 57, 57, 10, 57, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 10, 129, 163, 163, 201, 201, 201, 201, 201, 129, 57, 10, 1, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) total number of confs: 946 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919061 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919061 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919061/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919061 Building REAL300004919062 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919062' /scratch/stefan/7775247/working/building/REAL300004919062 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919062 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919062/0 /scratch/stefan/7775247/working/building/REAL300004919062 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/62 `/scratch/stefan/7775247/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC(C1=CC=CC=C1)C(C)C)C(=O)[O-]) `REAL300004919062.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919062 none CC#CCC(NC(=O)CC(C1=CC=CC=C1)C(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [171, 171, 171, 88, 39, 39, 10, 39, 3, 1, 1, 1, 1, 1, 1, 1, 3, 8, 7, 88, 119, 119, 171, 171, 171, 171, 171, 88, 39, 10, 10, 3, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8] 201 rigid atoms, others: [32, 33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 854 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919062 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919062 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919062/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919062 Building REAL300004919063 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919063' /scratch/stefan/7775247/working/building/REAL300004919063 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919063 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919063/0 /scratch/stefan/7775247/working/building/REAL300004919063 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/63 `/scratch/stefan/7775247/working/3D/63' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(S(C)(=O)=O)=CC=C1Br)C(=O)[O-]) `REAL300004919063.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919063 none CC#CCC(NC(=O)C1=CC(S(C)(=O)=O)=CC=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 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: [73, 73, 73, 28, 7, 7, 1, 7, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 28, 43, 43, 73, 73, 73, 73, 73, 28, 7, 1, 3, 3, 3, 1, 1] 126 rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 348 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919063 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919063 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919063/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919063 Building REAL300004919064 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919064' /scratch/stefan/7775247/working/building/REAL300004919064 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919064 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919064/0 /scratch/stefan/7775247/working/building/REAL300004919064 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/64 `/scratch/stefan/7775247/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)C1=CC=C2OCCOC2=C1)C(=O)[O-]) `REAL300004919064.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919064 none CC#CCC(NC(=O)C(C)C1=CC=C2OCCOC2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 5, 1, 1, 1, 1, 12, 5, 5, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 100, 50, 49, 12, 49, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 100, 136, 136, 201, 201, 201, 201, 201, 100, 49, 12, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 977 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919064 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919064 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919064/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919064 Building REAL300004919065 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919065' /scratch/stefan/7775247/working/building/REAL300004919065 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919065 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919065/0 /scratch/stefan/7775247/working/building/REAL300004919065 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/65 `/scratch/stefan/7775247/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N=C(CC(C)C)S1)C(=O)[O-]) `REAL300004919065.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919065 none CC#CCC(NC(=O)C1=C(C)N=C(CC(C)C)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 8, 1, 5, 5, 5, 5, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 38, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 38, 62, 62, 103, 103, 103, 103, 103, 38, 10, 2, 2, 2, 5, 5, 8, 8, 8, 8, 8, 8, 8] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 17] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 534 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919065 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919065 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919065/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919065 Building REAL300004919066 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919066' /scratch/stefan/7775247/working/building/REAL300004919066 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919066 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919066/0 /scratch/stefan/7775247/working/building/REAL300004919066 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/66 `/scratch/stefan/7775247/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(CC2CC2)C(C)=C1)C(=O)[O-]) `REAL300004919066.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919066 none CC#CCC(NC(=O)C1=C(C)N(CC2CC2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 8, 5, 5, 5, 5, 1, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 39, 13, 13, 1, 13, 1, 1, 1, 1, 1, 3, 10, 10, 1, 1, 1, 39, 58, 58, 99, 99, 99, 99, 99, 39, 13, 2, 2, 2, 3, 3, 10, 10, 10, 10, 10, 2, 2, 2, 1] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 16, 17, 18, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 505 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919066 none CC#CCC(NC(=O)C1=C(C)N(CC2CC2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 8, 5, 5, 5, 5, 1, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 110, 60, 60, 10, 60, 10, 10, 10, 5, 1, 1, 1, 1, 10, 10, 10, 110, 146, 146, 201, 201, 201, 201, 201, 110, 60, 10, 10, 10, 5, 5, 1, 1, 1, 1, 1, 10, 10, 10, 10] 201 rigid atoms, others: [34, 35, 36, 37, 38, 12, 13, 14, 15] 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, 39, 40, 41, 42]) total number of confs: 948 number of broken/clashed sets: 45 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919066 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919066 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919066/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919066 Building REAL300004919067 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919067' /scratch/stefan/7775247/working/building/REAL300004919067 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919067 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919067/0 /scratch/stefan/7775247/working/building/REAL300004919067 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/67 `/scratch/stefan/7775247/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CC=C(OC(F)F)C=C2)S1)C(=O)[O-]) `REAL300004919067.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919067 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(OC(F)F)C=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 6, 6, 1, 1, 12, 55, 55, 6, 6, 1, 11, 17, 17, 23, 23, 23, 23, 23, 11, 7, 1, 1, 6, 6, 55, 6, 6] 201 rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 12, 22] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) 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: REAL300004919067 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(OC(F)F)C=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 33, 19, 19, 6, 19, 6, 6, 6, 1, 1, 1, 1, 1, 1, 11, 27, 27, 1, 1, 6, 33, 49, 49, 68, 68, 68, 68, 68, 33, 19, 6, 6, 1, 1, 27, 1, 1] 201 rigid atoms, others: [35, 36, 38, 39, 11, 12, 13, 14, 15, 16, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37]) total number of confs: 427 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919067 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919067 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919067/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919067 Building REAL300004919068 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919068' /scratch/stefan/7775247/working/building/REAL300004919068 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919068 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919068/0 /scratch/stefan/7775247/working/building/REAL300004919068 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/68 `/scratch/stefan/7775247/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(=O)NCCCC1=CC=CC=C1)C(=O)[O-]) `REAL300004919068.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919068 none CC#CCC(NC(=O)C(=O)NCCCC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [138, 138, 138, 113, 58, 58, 37, 60, 37, 37, 8, 6, 4, 1, 1, 1, 1, 1, 1, 1, 113, 117, 117, 138, 138, 138, 138, 138, 113, 60, 37, 8, 8, 6, 6, 4, 4, 1, 1, 1, 1, 1] 138 rigid atoms, others: [37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 595 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919068 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919068 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919068/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919068 Building REAL300004919069 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919069' /scratch/stefan/7775247/working/building/REAL300004919069 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919069 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919069/0 /scratch/stefan/7775247/working/building/REAL300004919069 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/69 `/scratch/stefan/7775247/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=C(Cl)C=CC=C2Cl)C(C)=N1)C(=O)[O-]) `REAL300004919069.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919069 none CC#CCC(NC(=O)C1=NN(C2=C(Cl)C=CC=C2Cl)C(C)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 16, 1, 1, 1, 1, 16, 1, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 39, 12, 12, 1, 12, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 39, 54, 54, 81, 81, 81, 81, 81, 39, 13, 4, 4, 4, 2, 2, 2] 86 rigid atoms, others: [6, 8, 9, 10, 11, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 400 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919069 none CC#CCC(NC(=O)C1=NN(C2=C(Cl)C=CC=C2Cl)C(C)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 16, 1, 1, 1, 1, 16, 1, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 45, 18, 18, 3, 18, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 45, 61, 61, 86, 86, 86, 86, 86, 45, 18, 1, 1, 1, 4, 4, 4] 86 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 416 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919069 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919069 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919069/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919069 Building REAL300004919070 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919070' /scratch/stefan/7775247/working/building/REAL300004919070 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919070 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919070/0 /scratch/stefan/7775247/working/building/REAL300004919070 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/70 `/scratch/stefan/7775247/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Cl)=C(OCC(C)C)C(OC)=C1)C(=O)[O-]) `REAL300004919070.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919070 none CC#CCC(NC(=O)C1=CC(Cl)=C(OCC(C)C)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 16, 1, 12, 5, 5, 5, 5, 1, 12, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 2, 6, 9, 11, 1, 1, 3, 1, 13, 21, 21, 38, 38, 38, 38, 38, 13, 5, 1, 6, 6, 11, 11, 11, 11, 11, 11, 11, 4, 4, 4, 1] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 45, 18, 19, 21] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919070 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919070 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919070/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919070 Building REAL300004919071 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919071' /scratch/stefan/7775247/working/building/REAL300004919071 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919071 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919071/0 /scratch/stefan/7775247/working/building/REAL300004919071 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/71 `/scratch/stefan/7775247/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OCC)C(OC)=C1)C(=O)[O-]) `REAL300004919071.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919071 none CC#CCC(NC(=O)C1=CC=C(OCC)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 9, 31, 1, 1, 3, 1, 13, 22, 22, 40, 40, 40, 40, 40, 13, 5, 1, 1, 31, 31, 31, 31, 31, 3, 3, 3, 1] 201 rigid atoms, others: [6, 39, 8, 9, 10, 11, 12, 15, 16, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 296 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919071 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919071 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919071/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919071 Building REAL300004919072 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919072' /scratch/stefan/7775247/working/building/REAL300004919072 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919072 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919072/0 /scratch/stefan/7775247/working/building/REAL300004919072 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/72 `/scratch/stefan/7775247/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(N(C)C)C([N+](=O)[O-])=C1)C(=O)[O-]) `REAL300004919072.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919072 none CC#CCC(NC(=O)C1=CC=C(N(C)C)C([N+](=O)[O-])=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 1, 8, 11, 11, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 3, 3, 1, 1, 2, 2, 1, 25, 38, 38, 72, 72, 72, 72, 72, 25, 7, 1, 1, 4, 4, 4, 4, 4, 4, 1] 72 rigid atoms, others: [38, 6, 8, 9, 10, 11, 12, 15, 16, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 356 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919072 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919072 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919072/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919072 Building REAL300004919073 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919073' /scratch/stefan/7775247/working/building/REAL300004919073 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919073 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919073/0 /scratch/stefan/7775247/working/building/REAL300004919073 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/73 `/scratch/stefan/7775247/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CSCC(=O)NC1=CC=C(C)C=C1)C(=O)[O-]) `REAL300004919073.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919073 none CC#CCC(NC(=O)CSCC(=O)NC1=CC=C(C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 14, 5, 1, 11, 8, 1, 1, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 125, 63, 63, 46, 63, 38, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 125, 151, 151, 189, 189, 189, 189, 189, 124, 63, 46, 46, 13, 13, 3, 1, 1, 2, 2, 2, 1, 1] 189 rigid atoms, others: [36, 37, 41, 42, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 937 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919073 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919073 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919073/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919073 Building REAL300004919074 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919074' /scratch/stefan/7775247/working/building/REAL300004919074 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919074 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919074/0 /scratch/stefan/7775247/working/building/REAL300004919074 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/74 `/scratch/stefan/7775247/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC(Cl)=C(OCC)C(OC)=C1)C(=O)[O-]) `REAL300004919074.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919074 none CC#CCC(NC(=O)C=CC1=CC(Cl)=C(OCC)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 98, 48, 22, 22, 5, 22, 5, 1, 1, 1, 1, 1, 1, 1, 3, 9, 1, 1, 4, 1, 48, 75, 75, 98, 98, 98, 98, 98, 48, 22, 5, 5, 1, 9, 9, 9, 9, 9, 4, 4, 4, 1] 201 rigid atoms, others: [34, 43, 9, 10, 11, 12, 13, 14, 15, 18, 19, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 528 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919074 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919074 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919074/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919074 Building REAL300004919075 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919075' /scratch/stefan/7775247/working/building/REAL300004919075 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919075 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919075/0 /scratch/stefan/7775247/working/building/REAL300004919075 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/75 `/scratch/stefan/7775247/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Cl)=C(OCCC)C(OC)=C1)C(=O)[O-]) `REAL300004919075.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919075 none CC#CCC(NC(=O)C1=CC(Cl)=C(OCCC)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 16, 1, 12, 5, 5, 5, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 2, 8, 16, 1, 1, 3, 1, 13, 21, 21, 40, 40, 40, 40, 40, 13, 5, 1, 8, 8, 18, 18, 19, 19, 19, 4, 4, 4, 1] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 17, 18, 20, 42, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919075 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919075 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919075/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919075 Building REAL300004919076 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919076' /scratch/stefan/7775247/working/building/REAL300004919076 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919076 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919076/0 /scratch/stefan/7775247/working/building/REAL300004919076 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/76 `/scratch/stefan/7775247/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Cl)=C(OCCC(C)C)C(OC)=C1)C(=O)[O-]) `REAL300004919076.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919076 none CC#CCC(NC(=O)C1=CC(Cl)=C(OCCC(C)C)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 16, 1, 12, 5, 5, 5, 5, 5, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 2, 8, 13, 14, 14, 1, 1, 3, 1, 13, 20, 20, 36, 36, 36, 36, 36, 13, 5, 1, 8, 8, 13, 13, 14, 14, 14, 14, 14, 14, 14, 4, 4, 4, 1] 201 rigid atoms, others: [33, 6, 8, 9, 10, 11, 12, 13, 48, 19, 20, 22] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 242 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919076 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919076 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919076/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919076 Building REAL300004919077 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919077' /scratch/stefan/7775247/working/building/REAL300004919077 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919077 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919077/0 /scratch/stefan/7775247/working/building/REAL300004919077 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/77 `/scratch/stefan/7775247/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Cl)=C(OCCCC)C(OCC)=C1)C(=O)[O-]) `REAL300004919077.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919077 none CC#CCC(NC(=O)C1=CC(Cl)=C(OCCCC)C(OCC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 16, 1, 12, 5, 5, 5, 5, 1, 12, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 2, 8, 16, 16, 1, 1, 6, 7, 1, 11, 16, 16, 23, 23, 23, 23, 23, 11, 5, 1, 8, 8, 16, 16, 17, 17, 17, 16, 16, 7, 7, 8, 8, 8, 1] 201 rigid atoms, others: [33, 6, 8, 9, 10, 11, 12, 13, 48, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919077 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919077 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919077/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919077 Building REAL300004919078 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919078' /scratch/stefan/7775247/working/building/REAL300004919078 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919078 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919078/0 /scratch/stefan/7775247/working/building/REAL300004919078 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/78 `/scratch/stefan/7775247/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC([N+](=O)[O-])=CC=C1N(C)C)C(=O)[O-]) `REAL300004919078.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919078 none CC#CCC(NC(=O)C1=CC([N+](=O)[O-])=CC=C1N(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 8, 11, 11, 1, 1, 1, 8, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 28, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 28, 40, 40, 60, 60, 60, 60, 60, 28, 12, 1, 1, 1, 4, 4, 4, 3, 3, 3] 60 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 298 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919078 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919078 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919078/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919078 Building REAL300004919079 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919079' /scratch/stefan/7775247/working/building/REAL300004919079 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919079 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919079/0 /scratch/stefan/7775247/working/building/REAL300004919079 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/79 `/scratch/stefan/7775247/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(Br)S1)C(=O)[O-]) `REAL300004919079.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919079 none CC#CCC(NC(=O)C=CC1=CC=C(Br)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 17, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 74, 74, 12, 74, 12, 1, 1, 1, 1, 1, 1, 1, 137, 163, 163, 201, 201, 201, 201, 201, 137, 74, 12, 12, 1, 1] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 862 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919079 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919079 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919079/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919079 Building REAL300004919080 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919080' /scratch/stefan/7775247/working/building/REAL300004919080 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919080 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919080/0 /scratch/stefan/7775247/working/building/REAL300004919080 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/80 `/scratch/stefan/7775247/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(S(C)(=O)=O)=CC=C1Cl)C(=O)[O-]) `REAL300004919080.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919080 none CC#CCC(NC(=O)C1=CC(S(C)(=O)=O)=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 28, 7, 7, 1, 7, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 28, 42, 42, 75, 75, 75, 75, 75, 28, 7, 1, 3, 3, 3, 1, 1] 127 rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 350 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919080 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919080 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919080/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919080 Building REAL300004919081 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919081' /scratch/stefan/7775247/working/building/REAL300004919081 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919081 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919081/0 /scratch/stefan/7775247/working/building/REAL300004919081 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/81 `/scratch/stefan/7775247/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCCC1C(=O)N1C2=CC=CC=C2CC1C)C(=O)[O-]) `REAL300004919081.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919081 none CC#CCC(NC(=O)C1CCCCC1C(=O)N1C2=CC=CC=C2CC1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 20, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 32, 32, 39, 39, 39, 39, 39, 20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 47 rigid atoms, others: [45, 43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 218 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: REAL300004919081 none CC#CCC(NC(=O)C1CCCCC1C(=O)N1C2=CC=CC=C2CC1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 28, 14, 14, 4, 14, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 37, 37, 47, 47, 47, 47, 47, 28, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 47 rigid atoms, others: [48, 51, 49, 50, 14, 47, 16, 17, 18, 19, 20, 46, 22, 23, 24, 25, 52, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 53, 54, 55]) total number of confs: 238 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919081 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919081 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919081/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919081 Building REAL300004919082 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919082' /scratch/stefan/7775247/working/building/REAL300004919082 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919082 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919082/0 /scratch/stefan/7775247/working/building/REAL300004919082 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/82 `/scratch/stefan/7775247/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(OC(C)C)C(OC)=C1)C(=O)[O-]) `REAL300004919082.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919082 none CC#CCC(NC(=O)C=CC1=CC=C(OC(C)C)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 38, 18, 18, 5, 18, 5, 1, 1, 1, 1, 1, 1, 7, 13, 13, 1, 1, 3, 1, 38, 58, 58, 82, 82, 82, 82, 82, 38, 18, 5, 5, 1, 1, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 1] 201 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 18, 19, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 468 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919082 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919082 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919082/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919082 Building REAL300004919083 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919083' /scratch/stefan/7775247/working/building/REAL300004919083 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919083 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919083/0 /scratch/stefan/7775247/working/building/REAL300004919083 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/83 `/scratch/stefan/7775247/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CSCC(=O)NC1=NOC(C)=C1)C(=O)[O-]) `REAL300004919083.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919083 none CC#CCC(NC(=O)CSCC(=O)NC1=NOC(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 14, 5, 1, 11, 8, 1, 8, 12, 1, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 86, 86, 58, 86, 40, 15, 3, 4, 4, 1, 1, 1, 1, 1, 1, 1, 150, 170, 170, 201, 201, 201, 201, 201, 150, 86, 58, 58, 15, 15, 4, 2, 2, 2, 1] 201 rigid atoms, others: [38, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 951 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919083 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919083 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919083/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919083 Building REAL300004919084 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919084' /scratch/stefan/7775247/working/building/REAL300004919084 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919084 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919084/0 /scratch/stefan/7775247/working/building/REAL300004919084 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/84 `/scratch/stefan/7775247/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CSC(N(C(C)=O)C2=CC=CC=C2)=N1)C(=O)[O-]) `REAL300004919084.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919084 none CC#CCC(NC(=O)C=CC1=CSC(N(C(C)=O)C2=CC=CC=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 14, 1, 8, 1, 5, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [47, 47, 47, 26, 15, 15, 3, 14, 3, 1, 1, 1, 1, 1, 1, 5, 17, 17, 5, 11, 11, 7, 11, 11, 1, 26, 31, 31, 47, 47, 47, 47, 47, 26, 15, 3, 3, 1, 17, 17, 17, 11, 11, 7, 11, 11] 87 rigid atoms, others: [37, 9, 10, 11, 12, 13, 14, 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, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919084 none CC#CCC(NC(=O)C=CC1=CSC(N(C(C)=O)C2=CC=CC=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 14, 1, 8, 1, 5, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [80, 80, 80, 55, 42, 42, 20, 42, 20, 11, 11, 11, 11, 6, 1, 6, 16, 16, 1, 1, 1, 1, 1, 1, 11, 55, 63, 63, 80, 80, 80, 80, 80, 55, 42, 20, 20, 11, 16, 16, 16, 1, 1, 1, 1, 1] 87 rigid atoms, others: [41, 42, 43, 44, 45, 14, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 368 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919084 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919084 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919084/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919084 Building REAL300004919085 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919085' /scratch/stefan/7775247/working/building/REAL300004919085 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919085 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919085/0 /scratch/stefan/7775247/working/building/REAL300004919085 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/85 `/scratch/stefan/7775247/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CSC(C2=CC=C(OC)C(OC)=C2)=N1)C(=O)[O-]) `REAL300004919085.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919085 none CC#CCC(NC(=O)CC1=CSC(C2=CC=C(OC)C(OC)=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 14, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 39, 23, 23, 5, 23, 1, 1, 1, 1, 1, 1, 5, 5, 4, 4, 13, 5, 5, 13, 5, 1, 39, 42, 42, 63, 63, 63, 63, 63, 39, 23, 5, 5, 1, 5, 5, 13, 13, 13, 13, 13, 13, 5] 201 rigid atoms, others: [36, 8, 9, 10, 11, 12, 13, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 300 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919085 none CC#CCC(NC(=O)CC1=CSC(C2=CC=C(OC)C(OC)=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 14, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 146, 116, 66, 66, 17, 66, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 3, 1, 1, 3, 1, 5, 116, 116, 116, 146, 146, 146, 146, 146, 116, 66, 17, 17, 5, 1, 1, 4, 4, 4, 3, 3, 3, 1] 201 rigid atoms, others: [45, 37, 38, 12, 13, 14, 15, 16, 17, 19, 20, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 600 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919085 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919085 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919085/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919085 Building REAL300004919086 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919086' /scratch/stefan/7775247/working/building/REAL300004919086 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919086 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919086/0 /scratch/stefan/7775247/working/building/REAL300004919086 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/86 `/scratch/stefan/7775247/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(S(N)(=O)=O)=CC=C1OC)C(=O)[O-]) `REAL300004919086.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919086 none CC#CCC(NC(=O)C1=CC(S(N)(=O)=O)=CC=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 14, 8, 11, 11, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 33, 12, 12, 1, 12, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 3, 33, 50, 50, 80, 80, 80, 80, 80, 33, 12, 1, 5, 5, 1, 1, 3, 3, 3] 201 rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 35, 36, 37]) total number of confs: 403 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919086 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919086 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919086/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919086 Building REAL300004919087 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919087' /scratch/stefan/7775247/working/building/REAL300004919087 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919087 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919087/0 /scratch/stefan/7775247/working/building/REAL300004919087 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/87 `/scratch/stefan/7775247/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(OC(F)F)C(OCC)=C1)C(=O)[O-]) `REAL300004919087.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919087 none CC#CCC(NC(=O)C=CC1=CC=C(OC(F)F)C(OCC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 12, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 27, 17, 17, 5, 17, 5, 1, 1, 1, 1, 1, 1, 7, 12, 12, 1, 1, 9, 13, 1, 27, 37, 37, 56, 56, 56, 56, 56, 27, 17, 5, 5, 1, 1, 12, 13, 13, 13, 13, 13, 1] 201 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 43, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42]) total number of confs: 330 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919087 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919087 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919087/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919087 Building REAL300004919088 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919088' /scratch/stefan/7775247/working/building/REAL300004919088 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919088 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919088/0 /scratch/stefan/7775247/working/building/REAL300004919088 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/88 `/scratch/stefan/7775247/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)SCC(=O)NC1=CC=C(F)C=C1)C(=O)[O-]) `REAL300004919088.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919088 none CC#CCC(NC(=O)C(C)SCC(=O)NC1=CC=C(F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 5, 14, 5, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 98, 87, 49, 49, 36, 49, 30, 36, 12, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 87, 90, 90, 98, 98, 98, 98, 98, 87, 49, 36, 36, 36, 36, 12, 12, 3, 1, 1, 1, 1] 98 rigid atoms, others: [39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 412 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919088 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919088 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919088/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919088 Building REAL300004919089 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919089' /scratch/stefan/7775247/working/building/REAL300004919089 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919089 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919089/0 /scratch/stefan/7775247/working/building/REAL300004919089 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/89 `/scratch/stefan/7775247/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC(Cl)=C(OCCC)C(OCC)=C1)C(=O)[O-]) `REAL300004919089.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919089 none CC#CCC(NC(=O)C=CC1=CC(Cl)=C(OCCC)C(OCC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 5, 1, 12, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 27, 27, 27, 5, 27, 5, 1, 1, 1, 1, 1, 1, 1, 3, 9, 17, 1, 1, 9, 24, 1, 27, 27, 27, 51, 51, 51, 51, 51, 27, 27, 5, 5, 1, 9, 9, 20, 20, 20, 20, 20, 24, 24, 24, 24, 24, 1] 201 rigid atoms, others: [36, 9, 10, 11, 12, 13, 14, 15, 49, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 360 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919089 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919089 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919089/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919089 Building REAL300004919090 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919090' /scratch/stefan/7775247/working/building/REAL300004919090 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919090 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919090/0 /scratch/stefan/7775247/working/building/REAL300004919090 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/90 `/scratch/stefan/7775247/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(COC2=CC=CC=C2)O1)C(=O)[O-]) `REAL300004919090.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919090 none CC#CCC(NC(=O)C1=CC=C(COC2=CC=CC=C2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 12, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 23, 8, 9, 1, 9, 1, 1, 1, 1, 1, 8, 13, 14, 14, 13, 14, 14, 1, 23, 37, 37, 70, 70, 70, 70, 70, 23, 9, 1, 1, 8, 8, 14, 14, 13, 14, 14] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 365 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: REAL300004919090 none CC#CCC(NC(=O)C1=CC=C(COC2=CC=CC=C2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 12, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 107, 53, 53, 14, 53, 14, 14, 14, 6, 2, 1, 1, 1, 1, 1, 1, 1, 14, 107, 140, 140, 201, 201, 201, 201, 201, 107, 53, 14, 14, 6, 6, 1, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 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]) total number of confs: 965 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919090 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919090 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919090/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919090 Building REAL300004919091 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919091' /scratch/stefan/7775247/working/building/REAL300004919091 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919091 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919091/0 /scratch/stefan/7775247/working/building/REAL300004919091 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/91 `/scratch/stefan/7775247/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1[N-]S(C)(=O)=O)C(=O)[O-]) `REAL300004919091.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919091/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919091 none CC#CCC(NC(=O)C1=CC=CC=C1[N-]S(C)(=O)=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 5, 11, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 2, 2, 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: [7, 7, 7, 4, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 4, 4, 4, 7, 7, 7, 7, 7, 4, 3, 1, 1, 1, 1, 3, 3, 3] 9 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919091 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919091 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919091/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919091 Building REAL300004919092 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919092' /scratch/stefan/7775247/working/building/REAL300004919092 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919092 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919092/0 /scratch/stefan/7775247/working/building/REAL300004919092 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/92 `/scratch/stefan/7775247/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(CS(=O)(=O)C2=CC=CC=C2)O1)C(=O)[O-]) `REAL300004919092.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919092 none CC#CCC(NC(=O)C1=CC=C(CS(=O)(=O)C2=CC=CC=C2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 6, 7, 1, 7, 1, 1, 1, 1, 1, 5, 30, 30, 30, 30, 30, 30, 30, 30, 1, 15, 24, 24, 45, 45, 45, 45, 45, 15, 7, 1, 1, 5, 5, 30, 30, 30, 30, 30] 201 rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 12, 22] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 319 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919092 none CC#CCC(NC(=O)C1=CC=C(CS(=O)(=O)C2=CC=CC=C2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 12, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 122, 68, 68, 30, 68, 30, 30, 30, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 122, 154, 154, 201, 201, 201, 201, 201, 122, 68, 30, 30, 10, 10, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 960 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919092 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919092 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919092/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919092 Building REAL300004919093 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919093' /scratch/stefan/7775247/working/building/REAL300004919093 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919093 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919093/0 /scratch/stefan/7775247/working/building/REAL300004919093 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/93 `/scratch/stefan/7775247/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCNS(=O)(=O)C1=CC=C(F)C=C1)C(=O)[O-]) `REAL300004919093.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919093 none CC#CCC(NC(=O)CCNS(=O)(=O)C1=CC=C(F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1] 3 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 7 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919093 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919093 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919093/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919093 Building REAL300004919094 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919094' /scratch/stefan/7775247/working/building/REAL300004919094 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919094 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919094/0 /scratch/stefan/7775247/working/building/REAL300004919094 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/94 `/scratch/stefan/7775247/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(C2=CC=C(C)C=C2)N=C1C1=CC=CC=C1)C(=O)[O-]) `REAL300004919094.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919094 none CC#CCC(NC(=O)C1=CN(C2=CC=C(C)C=C2)N=C1C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 158, 54, 12, 12, 1, 12, 1, 1, 1, 1, 4, 4, 1, 1, 4, 4, 1, 1, 1, 7, 7, 2, 7, 7, 54, 84, 84, 158, 158, 158, 158, 158, 54, 12, 1, 4, 4, 4, 4, 4, 4, 4, 7, 7, 6, 7, 7] 201 rigid atoms, others: [36, 6, 8, 9, 10, 11, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 770 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: REAL300004919094 none CC#CCC(NC(=O)C1=CN(C2=CC=C(C)C=C2)N=C1C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 106, 41, 41, 7, 41, 7, 7, 7, 7, 17, 17, 7, 7, 17, 17, 7, 1, 1, 1, 1, 1, 1, 1, 106, 140, 140, 200, 200, 200, 200, 200, 106, 41, 7, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 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]) total number of confs: 1010 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: REAL300004919094 none CC#CCC(NC(=O)C1=CN(C2=CC=C(C)C=C2)N=C1C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [185, 185, 185, 86, 36, 36, 4, 36, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 17, 17, 6, 17, 17, 86, 121, 121, 185, 185, 185, 185, 185, 86, 36, 4, 1, 1, 2, 2, 2, 1, 1, 17, 17, 17, 17, 17] 201 rigid atoms, others: [43, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 44, 45, 46, 47, 48]) total number of confs: 925 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919094 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919094 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919094/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919094 Building REAL300004919095 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919095' /scratch/stefan/7775247/working/building/REAL300004919095 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919095 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919095/0 /scratch/stefan/7775247/working/building/REAL300004919095 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/95 `/scratch/stefan/7775247/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCN1S(C)(=O)=O)C(=O)[O-]) `REAL300004919095.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919095 none CC#CCC(NC(=O)C1CCCN1S(C)(=O)=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 5, 5, 8, 14, 5, 11, 11, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 2, 2, 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: [62, 62, 62, 25, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 6, 6, 6, 25, 40, 40, 62, 62, 62, 62, 62, 25, 9, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7] 74 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36]) total number of confs: 322 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919095 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919095 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919095/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919095 Building REAL300004919096 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919096' /scratch/stefan/7775247/working/building/REAL300004919096 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919096 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919096/0 /scratch/stefan/7775247/working/building/REAL300004919096 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/96 `/scratch/stefan/7775247/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC)C(S(=O)(=O)N(CC)CC)=C1)C(=O)[O-]) `REAL300004919096.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919096 none CC#CCC(NC(=O)C1=CC=C(OC)C(S(=O)(=O)N(CC)CC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 3, 1, 1, 6, 6, 6, 11, 29, 11, 25, 1, 10, 17, 17, 32, 32, 32, 32, 32, 10, 4, 1, 1, 3, 3, 3, 29, 29, 29, 29, 29, 25, 25, 25, 25, 25, 1] 201 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 14, 15, 49, 23] set([0, 1, 2, 3, 4, 5, 7, 13, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 342 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919096 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919096 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919096/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919096 Building REAL300004919097 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919097' /scratch/stefan/7775247/working/building/REAL300004919097 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919097 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919097/0 /scratch/stefan/7775247/working/building/REAL300004919097 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/97 `/scratch/stefan/7775247/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC)C(S(=O)(=O)NC(C)C)=C1)C(=O)[O-]) `REAL300004919097.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919097 none CC#CCC(NC(=O)C1=CC=C(OC)C(S(=O)(=O)NC(C)C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 3, 1, 1, 7, 7, 7, 17, 26, 26, 1, 17, 26, 26, 59, 59, 59, 59, 59, 17, 5, 1, 1, 3, 3, 3, 17, 26, 26, 26, 26, 26, 26, 26, 1] 201 rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 12, 14, 15, 46, 22] set([0, 1, 2, 3, 4, 5, 7, 13, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 357 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919097 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919097 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919097/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919097 Building REAL300004919098 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919098' /scratch/stefan/7775247/working/building/REAL300004919098 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919098 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919098/0 /scratch/stefan/7775247/working/building/REAL300004919098 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/98 `/scratch/stefan/7775247/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(S(=O)(=O)N(CC)CC)=CC=C1C)C(=O)[O-]) `REAL300004919098.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919098 none CC#CCC(NC(=O)C1=CC(S(=O)(=O)N(CC)CC)=CC=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 9, 6, 6, 1, 6, 1, 1, 1, 1, 8, 8, 8, 18, 30, 18, 31, 1, 1, 1, 1, 9, 15, 15, 24, 24, 24, 24, 24, 9, 6, 1, 30, 30, 30, 30, 30, 31, 31, 31, 31, 31, 1, 1, 2, 2, 2] 201 rigid atoms, others: [33, 6, 8, 9, 10, 11, 44, 45, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 316 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919098 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919098 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919098/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919098 Building REAL300004919099 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919099' /scratch/stefan/7775247/working/building/REAL300004919099 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919099 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919099/0 /scratch/stefan/7775247/working/building/REAL300004919099 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/99 `/scratch/stefan/7775247/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC([N-]S(=O)(=O)C2=CC=CS2)=C1)C(=O)[O-]) `REAL300004919099.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919099 none CC#CCC(NC(=O)C1=CC=CC([N-]S(=O)(=O)C2=CC=CS2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 30, 30, 30, 30, 1, 14, 19, 19, 33, 33, 33, 33, 33, 14, 5, 1, 1, 1, 30, 30, 30, 1] 201 rigid atoms, others: [33, 34, 35, 6, 39, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919099 none CC#CCC(NC(=O)C1=CC=CC([N-]S(=O)(=O)C2=CC=CS2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 14, 11, 11, 1, 1, 1, 1, 14, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 127, 76, 76, 30, 76, 30, 30, 30, 30, 18, 6, 1, 6, 6, 1, 1, 1, 1, 1, 30, 127, 156, 156, 201, 201, 201, 201, 201, 127, 76, 30, 30, 30, 1, 1, 1, 30] 201 rigid atoms, others: [36, 37, 38, 14, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39]) total number of confs: 925 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919099 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919099 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919099/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919099 Building REAL300004919100 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919100' /scratch/stefan/7775247/working/building/REAL300004919100 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919100 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919100/0 /scratch/stefan/7775247/working/building/REAL300004919100 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/100 `/scratch/stefan/7775247/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCN(C(=O)CCC2=CC=CC=C2)CC1)C(=O)[O-]) `REAL300004919100.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919100 none CC#CCC(NC(=O)C1CCN(C(=O)CCC2=CC=CC=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 26, 12, 12, 1, 12, 1, 1, 1, 1, 1, 6, 6, 14, 14, 14, 14, 14, 14, 14, 1, 1, 26, 39, 39, 57, 57, 57, 57, 57, 26, 13, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 48, 49, 50, 51, 22, 23, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 337 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919100 none CC#CCC(NC(=O)C1CCN(C(=O)CCC2=CC=CC=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 117, 64, 64, 14, 64, 14, 14, 14, 7, 3, 7, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 117, 152, 152, 201, 201, 201, 201, 201, 117, 65, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14] 201 rigid atoms, others: [41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 48, 49, 50, 51]) total number of confs: 975 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919100 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919100 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919100/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919100 Building REAL300004919101 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919101' /scratch/stefan/7775247/working/building/REAL300004919101 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919101 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919101/0 /scratch/stefan/7775247/working/building/REAL300004919101 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/101 `/scratch/stefan/7775247/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC2CCCC2)C=C1)C(=O)[O-]) `REAL300004919101.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919101 none CC#CCC(NC(=O)C1=CC=C(OC2CCCC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 13, 37, 37, 37, 37, 1, 1, 9, 17, 17, 36, 36, 36, 36, 36, 9, 3, 1, 1, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 18, 19, 41, 42, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 249 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: REAL300004919101 none CC#CCC(NC(=O)C1=CC=C(OC2CCCC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 60, 60, 17, 60, 8, 37, 37, 8, 1, 1, 1, 1, 1, 1, 37, 37, 131, 156, 156, 201, 201, 201, 201, 201, 131, 60, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42]) total number of confs: 964 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919101 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919101 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919101/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919101 Building REAL300004919102 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919102' /scratch/stefan/7775247/working/building/REAL300004919102 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919102 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919102/0 /scratch/stefan/7775247/working/building/REAL300004919102 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/102 `/scratch/stefan/7775247/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OCC(F)(F)F)C=C1)C(=O)[O-]) `REAL300004919102.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919102 none CC#CCC(NC(=O)C1=CC=C(OCC(F)(F)F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 6, 24, 24, 24, 24, 1, 1, 10, 18, 18, 39, 39, 39, 39, 39, 10, 4, 1, 1, 24, 24, 1, 1] 201 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 251 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919102 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919102 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919102/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919102 Building REAL300004919103 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919103' /scratch/stefan/7775247/working/building/REAL300004919103 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919103 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919103/0 /scratch/stefan/7775247/working/building/REAL300004919103 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/103 `/scratch/stefan/7775247/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)SCC1=CC=CC=C1)C(=O)[O-]) `REAL300004919103.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919103 none CC#CCC(NC(=O)C(C)SCC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 5, 14, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 87, 71, 71, 38, 71, 16, 38, 4, 1, 1, 1, 1, 1, 1, 1, 87, 88, 88, 99, 99, 99, 99, 99, 87, 71, 38, 38, 38, 38, 4, 4, 1, 1, 1, 1, 1] 99 rigid atoms, others: [34, 35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 400 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919103 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919103 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919103/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919103 Building REAL300004919104 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919104' /scratch/stefan/7775247/working/building/REAL300004919104 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919104 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919104/0 /scratch/stefan/7775247/working/building/REAL300004919104 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/104 `/scratch/stefan/7775247/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)SC1=CC(Cl)=CC=C1Cl)C(=O)[O-]) `REAL300004919104.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919104 none CC#CCC(NC(=O)C(C)SC1=CC(Cl)=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 14, 1, 1, 1, 16, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 67, 67, 22, 67, 7, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 118, 154, 154, 201, 201, 201, 201, 201, 118, 67, 22, 22, 22, 22, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 994 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919104 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919104 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919104/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919104 Building REAL300004919105 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919105' /scratch/stefan/7775247/working/building/REAL300004919105 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919105 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919105/0 /scratch/stefan/7775247/working/building/REAL300004919105 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/105 `/scratch/stefan/7775247/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CSC1=CC=C(C(C)C)C=C1)C(=O)[O-]) `REAL300004919105.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919105 none CC#CCC(NC(=O)CSC1=CC=C(C(C)C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 14, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [164, 164, 164, 128, 79, 79, 20, 79, 4, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 128, 174, 174, 164, 164, 164, 164, 164, 128, 79, 21, 21, 1, 1, 3, 4, 4, 4, 4, 4, 4, 1, 1] 201 rigid atoms, others: [32, 40, 9, 10, 11, 12, 13, 14, 17, 18, 41, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 854 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919105 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919105 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919105/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919105 Building REAL300004919106 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919106' /scratch/stefan/7775247/working/building/REAL300004919106 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919106 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919106/0 /scratch/stefan/7775247/working/building/REAL300004919106 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/106 `/scratch/stefan/7775247/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(SCC2=CC=CC=C2)C=C1)C(=O)[O-]) `REAL300004919106.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919106 none CC#CCC(NC(=O)C1=CC=C(SCC2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 8, 35, 37, 37, 35, 37, 37, 1, 1, 8, 12, 12, 24, 24, 24, 24, 24, 8, 3, 1, 1, 35, 35, 37, 37, 35, 37, 37, 1, 1] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 20, 21, 41, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 233 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: REAL300004919106 none CC#CCC(NC(=O)C1=CC=C(SCC2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 120, 68, 68, 37, 68, 26, 37, 37, 9, 3, 1, 1, 1, 1, 1, 1, 1, 37, 37, 120, 154, 154, 201, 201, 201, 201, 201, 120, 68, 37, 37, 3, 3, 1, 1, 1, 1, 1, 37, 37] 201 rigid atoms, others: [36, 37, 38, 39, 40, 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, 41, 42]) total number of confs: 1004 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919106 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919106 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919106/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919106 Building REAL300004919107 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919107' /scratch/stefan/7775247/working/building/REAL300004919107 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919107 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919107/0 /scratch/stefan/7775247/working/building/REAL300004919107 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/107 `/scratch/stefan/7775247/working/3D/107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Cl)=CC=C1I)C(=O)[O-]) `REAL300004919107.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919107 none CC#CCC(NC(=O)C1=CC(Cl)=CC=C1I)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 1, 1, 18, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 24, 37, 37, 56, 56, 56, 56, 56, 24, 7, 1, 1, 1] 56 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 277 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919107 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919107 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919107/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919107 Building REAL300004919108 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919108' /scratch/stefan/7775247/working/building/REAL300004919108 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919108 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919108/0 /scratch/stefan/7775247/working/building/REAL300004919108 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/108 `/scratch/stefan/7775247/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(C)=C1I)C(=O)[O-]) `REAL300004919108.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919108 none CC#CCC(NC(=O)C1=CC=CC(C)=C1I)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'I', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 5, 1, 18, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 22, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 22, 34, 34, 53, 53, 53, 53, 53, 22, 7, 1, 1, 1, 2, 2, 2] 53 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 264 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919108 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919108 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919108/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919108 Building REAL300004919109 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919109' /scratch/stefan/7775247/working/building/REAL300004919109 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919109 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919109/0 /scratch/stefan/7775247/working/building/REAL300004919109 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/109 `/scratch/stefan/7775247/working/3D/109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(F)C=C1I)C(=O)[O-]) `REAL300004919109.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919109 none CC#CCC(NC(=O)C1=CC=C(F)C=C1I)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'I', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 18, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 22, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 22, 34, 34, 51, 51, 51, 51, 51, 22, 7, 1, 1, 1] 51 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 255 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919109 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919109 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919109/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919109 Building REAL300004919110 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919110' /scratch/stefan/7775247/working/building/REAL300004919110 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919110 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919110/0 /scratch/stefan/7775247/working/building/REAL300004919110 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/110 `/scratch/stefan/7775247/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(NC(=O)C2=CC=C(F)C=C2)=C1)C(=O)[O-]) `REAL300004919110.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919110 none CC#CCC(NC(=O)C1=CC=CC(NC(=O)C2=CC=C(F)C=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 8, 14, 14, 14, 14, 14, 14, 1, 17, 30, 30, 63, 63, 63, 63, 63, 17, 5, 1, 1, 1, 8, 14, 14, 14, 14, 1] 201 rigid atoms, others: [34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 23, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41]) total number of confs: 319 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919110 none CC#CCC(NC(=O)C1=CC=CC(NC(=O)C2=CC=C(F)C=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 98, 41, 41, 14, 41, 14, 14, 14, 14, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 14, 98, 136, 136, 201, 201, 201, 201, 201, 98, 41, 14, 14, 14, 3, 1, 1, 1, 1, 14] 201 rigid atoms, others: [38, 39, 40, 41, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42]) total number of confs: 965 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919110 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919110 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919110/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919110 Building REAL300004919111 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919111' /scratch/stefan/7775247/working/building/REAL300004919111 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919111 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919111/0 /scratch/stefan/7775247/working/building/REAL300004919111 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 111) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/111 `/scratch/stefan/7775247/working/3D/111' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(NC(=O)C2CCCCC2)=C1)C(=O)[O-]) `REAL300004919111.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919111 none CC#CCC(NC(=O)C1=CC=CC(NC(=O)C2CCCCC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 16, 16, 1, 14, 24, 24, 41, 41, 41, 41, 41, 14, 5, 1, 1, 1, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1] 201 rigid atoms, others: [33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 48, 22] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919111 none CC#CCC(NC(=O)C1=CC=CC(NC(=O)C2CCCCC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 51, 51, 16, 51, 16, 16, 16, 16, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 114, 149, 149, 201, 201, 201, 201, 201, 114, 51, 16, 16, 16, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 48]) total number of confs: 951 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919111 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919111 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919111/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919111 Building REAL300004919112 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919112' /scratch/stefan/7775247/working/building/REAL300004919112 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919112 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919112/0 /scratch/stefan/7775247/working/building/REAL300004919112 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/112 `/scratch/stefan/7775247/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC=CC=C1C(F)(F)F)C(=O)[O-]) `REAL300004919112.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919112 none CC#CCC(NC(=O)COC1=CC=CC=C1C(F)(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 130, 78, 78, 22, 78, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 130, 169, 169, 201, 201, 201, 201, 201, 130, 78, 22, 22, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16] 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]) total number of confs: 1052 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919112 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919112 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919112/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919112 Building REAL300004919113 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919113' /scratch/stefan/7775247/working/building/REAL300004919113 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919113 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919113/0 /scratch/stefan/7775247/working/building/REAL300004919113 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/113 `/scratch/stefan/7775247/working/3D/113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C(C)C2=CC=CC=C2)C(C)=C1)C(=O)[O-]) `REAL300004919113.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919113 none CC#CCC(NC(=O)C1=C(C)N(C(C)C2=CC=CC=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 18, 8, 8, 1, 8, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 18, 25, 25, 36, 36, 36, 36, 36, 18, 9, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1] 46 rigid atoms, others: [6, 8, 9, 10, 11, 12, 48, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 194 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: REAL300004919113 none CC#CCC(NC(=O)C1=C(C)N(C(C)C2=CC=CC=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 24, 12, 12, 3, 12, 3, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 24, 32, 32, 46, 46, 46, 46, 46, 24, 12, 3, 3, 3, 2, 2, 2, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3] 46 rigid atoms, others: [40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47, 48]) total number of confs: 222 number of broken/clashed sets: 46 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919113 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919113 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919113/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919113 Building REAL300004919114 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919114' /scratch/stefan/7775247/working/building/REAL300004919114 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919114 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919114/0 /scratch/stefan/7775247/working/building/REAL300004919114 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/114 `/scratch/stefan/7775247/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(OCC(F)(F)F)=CC=C1[N+](=O)[O-])C(=O)[O-]) `REAL300004919114.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919114 none CC#CCC(NC(=O)C1=CC(OCC(F)(F)F)=CC=C1[N+](=O)[O-])C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 1, 1, 8, 11, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 16, 6, 6, 1, 6, 1, 1, 1, 1, 6, 19, 19, 19, 19, 1, 1, 1, 1, 2, 2, 16, 29, 29, 51, 51, 51, 51, 51, 16, 6, 1, 19, 19, 1, 1] 201 rigid atoms, others: [33, 36, 37, 6, 8, 9, 10, 11, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35]) total number of confs: 309 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919114 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919114 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919114/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919114 Building REAL300004919115 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919115' /scratch/stefan/7775247/working/building/REAL300004919115 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919115 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919115/0 /scratch/stefan/7775247/working/building/REAL300004919115 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/115 `/scratch/stefan/7775247/working/3D/115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC([N+](=O)[O-])=CC=C1OC1=CC=C(OC)C=C1)C(=O)[O-]) `REAL300004919115.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919115 none CC#CCC(NC(=O)C1=CC([N+](=O)[O-])=CC=C1OC1=CC=C(OC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 8, 11, 11, 1, 1, 1, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 29, 12, 12, 1, 12, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 13, 13, 7, 8, 20, 13, 13, 29, 46, 46, 68, 68, 68, 68, 68, 29, 12, 1, 1, 1, 13, 13, 20, 20, 20, 13, 13] 201 rigid atoms, others: [36, 37, 6, 8, 9, 10, 11, 14, 15, 16, 17, 38] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 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]) total number of confs: 394 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919115 none CC#CCC(NC(=O)C1=CC([N+](=O)[O-])=CC=C1OC1=CC=C(OC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 8, 11, 11, 1, 1, 1, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [173, 173, 173, 91, 52, 52, 13, 52, 13, 13, 12, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 1, 2, 1, 1, 91, 131, 131, 173, 173, 173, 173, 173, 91, 52, 13, 13, 13, 1, 1, 2, 2, 2, 1, 1] 201 rigid atoms, others: [39, 40, 44, 45, 17, 18, 19, 20, 21, 22, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43]) total number of confs: 862 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919115 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919115 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919115/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919115 Building REAL300004919116 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919116' /scratch/stefan/7775247/working/building/REAL300004919116 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919116 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919116/0 /scratch/stefan/7775247/working/building/REAL300004919116 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/116 `/scratch/stefan/7775247/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(COC2=CC=CC=C2OC)O1)C(=O)[O-]) `REAL300004919116.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919116 none CC#CCC(NC(=O)C1=CC=C(COC2=CC=CC=C2OC)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 2, 1, 1, 1, 1, 1, 7, 33, 77, 77, 60, 77, 77, 77, 83, 1, 3, 5, 5, 7, 7, 7, 7, 7, 3, 2, 1, 1, 7, 7, 77, 77, 77, 77, 83, 83, 83] 201 rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 12, 22] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43]) 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: REAL300004919116 none CC#CCC(NC(=O)C1=CC=C(COC2=CC=CC=C2OC)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 128, 77, 77, 77, 77, 77, 77, 77, 31, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 77, 128, 141, 141, 201, 201, 201, 201, 201, 128, 77, 77, 77, 31, 31, 1, 1, 1, 1, 3, 3, 3] 201 rigid atoms, others: [37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43]) total number of confs: 931 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919116 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919116 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919116/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919116 Building REAL300004919117 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919117' /scratch/stefan/7775247/working/building/REAL300004919117 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919117 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919117/0 /scratch/stefan/7775247/working/building/REAL300004919117 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/117 `/scratch/stefan/7775247/working/3D/117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)OC1=CC=CC(C(C)(C)C)=C1)C(=O)[O-]) `REAL300004919117.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919117 none CC#CCC(NC(=O)C(C)OC1=CC=CC(C(C)(C)C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [141, 141, 141, 95, 78, 78, 26, 78, 11, 26, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 95, 106, 106, 141, 141, 141, 141, 141, 95, 78, 26, 26, 26, 26, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1] 201 rigid atoms, others: [35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 635 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919117 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919117 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919117/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919117 Building REAL300004919118 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919118' /scratch/stefan/7775247/working/building/REAL300004919118 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919118 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919118/0 /scratch/stefan/7775247/working/building/REAL300004919118 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/118 `/scratch/stefan/7775247/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=COC(Br)=C1)C(=O)[O-]) `REAL300004919118.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919118 none CC#CCC(NC(=O)C1=COC(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'Br', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 12, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 21, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 21, 33, 33, 46, 46, 46, 46, 46, 21, 6, 1, 1] 56 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919118 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919118 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919118/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919118 Building REAL300004919119 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919119' /scratch/stefan/7775247/working/building/REAL300004919119 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919119 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919119/0 /scratch/stefan/7775247/working/building/REAL300004919119 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/119 `/scratch/stefan/7775247/working/3D/119' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(S(=O)(=O)NC2=CC=CC=C2F)=CN1)C(=O)[O-]) `REAL300004919119.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919119 none CC#CCC(NC(=O)C1=CC(S(=O)(=O)NC2=CC=CC=C2F)=CN1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 6, 6, 1, 6, 1, 1, 1, 1, 3, 3, 3, 9, 23, 23, 23, 23, 23, 23, 1, 1, 17, 26, 26, 31, 31, 31, 31, 31, 17, 6, 1, 9, 23, 23, 23, 23, 1, 1] 201 rigid atoms, others: [34, 6, 8, 9, 10, 11, 40, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919119 none CC#CCC(NC(=O)C1=CC(S(=O)(=O)NC2=CC=CC=C2F)=CN1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 15, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 75, 75, 23, 75, 23, 23, 13, 5, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 131, 167, 167, 201, 201, 201, 201, 201, 131, 75, 23, 5, 1, 1, 1, 1, 23, 23] 201 rigid atoms, others: [36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41]) total number of confs: 979 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919119 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919119 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919119/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919119 Building REAL300004919120 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919120' /scratch/stefan/7775247/working/building/REAL300004919120 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919120 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919120/0 /scratch/stefan/7775247/working/building/REAL300004919120 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/120 `/scratch/stefan/7775247/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(S(=O)(=O)N2CCCCC2)=CN1C)C(=O)[O-]) `REAL300004919120.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919120 none CC#CCC(NC(=O)C1=CC(S(=O)(=O)N2CCCCC2)=CN1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 6, 6, 1, 6, 1, 1, 1, 1, 9, 9, 9, 39, 39, 39, 39, 39, 1, 1, 1, 13, 19, 19, 27, 27, 27, 27, 27, 13, 6, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 2, 2, 2] 201 rigid atoms, others: [33, 6, 8, 9, 10, 11, 44, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919120 none CC#CCC(NC(=O)C1=CC(S(=O)(=O)N2CCCCC2)=CN1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 1, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 147, 93, 93, 39, 93, 39, 39, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 39, 39, 39, 147, 172, 172, 201, 201, 201, 201, 201, 147, 93, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 14, 15, 16, 17, 18, 19, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 44, 45, 46, 47]) total number of confs: 864 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919120 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919120 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919120/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919120 Building REAL300004919121 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919121' /scratch/stefan/7775247/working/building/REAL300004919121 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919121 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919121/0 /scratch/stefan/7775247/working/building/REAL300004919121 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/121 `/scratch/stefan/7775247/working/3D/121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(N2C=NN=N2)C(C)=C1)C(=O)[O-]) `REAL300004919121.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919121 none CC#CCC(NC(=O)C1=CC=C(N2C=NN=N2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 8, 8, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 1, 26, 41, 41, 80, 80, 80, 80, 80, 26, 7, 1, 1, 8, 2, 2, 2, 1] 142 rigid atoms, others: [36, 6, 8, 9, 10, 11, 12, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 380 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919121 none CC#CCC(NC(=O)C1=CC=C(N2C=NN=N2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 8, 8, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [142, 142, 142, 74, 32, 32, 1, 32, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 74, 95, 95, 142, 142, 142, 142, 142, 74, 32, 8, 8, 1, 8, 8, 8, 8] 142 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36]) total number of confs: 664 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919121 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919121 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919121/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919121 Building REAL300004919122 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919122' /scratch/stefan/7775247/working/building/REAL300004919122 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919122 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919122/0 /scratch/stefan/7775247/working/building/REAL300004919122 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/122 `/scratch/stefan/7775247/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCSC1=CC=CC=C1Br)C(=O)[O-]) `REAL300004919122.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919122 none CC#CCC(NC(=O)CCSC1=CC=CC=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 14, 1, 1, 1, 1, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 154, 120, 120, 25, 120, 25, 8, 1, 1, 1, 1, 1, 1, 1, 1, 154, 192, 192, 201, 201, 201, 201, 201, 154, 120, 25, 25, 25, 25, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 919 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919122 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919122 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919122/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919122 Building REAL300004919123 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919123' /scratch/stefan/7775247/working/building/REAL300004919123 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919123 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919123/0 /scratch/stefan/7775247/working/building/REAL300004919123 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/123 `/scratch/stefan/7775247/working/3D/123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC=C(Cl)C=C1C1CCCCC1)C(=O)[O-]) `REAL300004919123.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919123 none CC#CCC(NC(=O)COC1=CC=C(Cl)C=C1C1CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 167, 112, 112, 32, 112, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 167, 180, 180, 200, 200, 200, 200, 200, 167, 112, 32, 32, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 201 rigid atoms, others: [35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 872 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919123 none CC#CCC(NC(=O)COC1=CC=C(Cl)C=C1C1CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 119, 119, 39, 119, 12, 4, 4, 4, 2, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 170, 181, 181, 201, 201, 201, 201, 201, 170, 119, 39, 39, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [48, 38, 39, 40, 41, 42, 43, 44, 45, 46, 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]) total number of confs: 851 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919123 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919123 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919123/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919123 Building REAL300004919124 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919124' /scratch/stefan/7775247/working/building/REAL300004919124 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919124 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919124/0 /scratch/stefan/7775247/working/building/REAL300004919124 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/124 `/scratch/stefan/7775247/working/3D/124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(S(=O)(=O)NCCC)C=C1)C(=O)[O-]) `REAL300004919124.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919124 none CC#CCC(NC(=O)C=CC1=CC=C(S(=O)(=O)NCCC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 14, 9, 9, 3, 9, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 21, 31, 1, 1, 14, 20, 20, 35, 35, 35, 35, 35, 14, 9, 3, 3, 1, 1, 5, 21, 21, 31, 31, 31, 31, 31, 1, 1] 201 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 45, 21, 22, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 306 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919124 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919124 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919124/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919124 Building REAL300004919125 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919125' /scratch/stefan/7775247/working/building/REAL300004919125 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919125 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919125/0 /scratch/stefan/7775247/working/building/REAL300004919125 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/125 `/scratch/stefan/7775247/working/3D/125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)OC1=CC=C(Cl)C(C)=C1)C(=O)[O-]) `REAL300004919125.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919125 none CC#CCC(NC(=O)C(C)OC1=CC=C(Cl)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 16, 1, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 111, 76, 76, 23, 76, 11, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 111, 158, 158, 201, 201, 201, 201, 201, 111, 76, 23, 23, 23, 23, 1, 1, 2, 2, 2, 1] 201 rigid atoms, others: [33, 34, 38, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 1048 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919125 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919125 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919125/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919125 Building REAL300004919126 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919126' /scratch/stefan/7775247/working/building/REAL300004919126 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919126 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919126/0 /scratch/stefan/7775247/working/building/REAL300004919126 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/126 `/scratch/stefan/7775247/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)SC1=CC=C(Br)C=C1)C(=O)[O-]) `REAL300004919126.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919126 none CC#CCC(NC(=O)C(C)SC1=CC=C(Br)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 14, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 66, 66, 17, 66, 6, 17, 1, 1, 1, 1, 1, 1, 1, 1, 119, 148, 148, 201, 201, 201, 201, 201, 119, 66, 17, 17, 17, 17, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 948 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919126 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919126 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919126/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919126 Building REAL300004919127 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919127' /scratch/stefan/7775247/working/building/REAL300004919127 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919127 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919127/0 /scratch/stefan/7775247/working/building/REAL300004919127 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 127) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/127 `/scratch/stefan/7775247/working/3D/127' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(CC2=CC=CC=C2)N=C1)C(=O)[O-]) `REAL300004919127.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919127 none CC#CCC(NC(=O)C1=C(C)N(CC2=CC=CC=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 29, 11, 11, 1, 11, 1, 1, 1, 1, 1, 5, 11, 11, 8, 11, 11, 1, 1, 29, 48, 48, 62, 62, 62, 62, 62, 29, 11, 2, 2, 2, 5, 5, 11, 11, 11, 11, 11, 1] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 19, 20, 41] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 373 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919127 none CC#CCC(NC(=O)C1=C(C)N(CC2=CC=CC=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 122, 66, 66, 11, 66, 11, 11, 11, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 122, 150, 150, 201, 201, 201, 201, 201, 122, 66, 12, 12, 12, 3, 3, 1, 1, 1, 1, 1, 11] 201 rigid atoms, others: [36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41]) total number of confs: 932 number of broken/clashed sets: 49 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919127 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919127 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919127/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919127 Building REAL300004919128 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919128' /scratch/stefan/7775247/working/building/REAL300004919128 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919128 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919128/0 /scratch/stefan/7775247/working/building/REAL300004919128 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/128 `/scratch/stefan/7775247/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=NC(C2=CC=C(OCC)C=C2)=NO1)C(=O)[O-]) `REAL300004919128.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919128 none CC#CCC(NC(=O)CCC1=NC(C2=CC=C(OCC)C=C2)=NO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 1, 8, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 58, 48, 48, 17, 48, 9, 1, 1, 1, 1, 1, 4, 4, 1, 2, 17, 32, 4, 4, 1, 1, 58, 71, 71, 99, 99, 99, 99, 99, 58, 48, 17, 17, 9, 9, 4, 4, 32, 32, 32, 32, 32, 4, 4] 201 rigid atoms, others: [9, 10, 11, 12, 13, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 547 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919128 none CC#CCC(NC(=O)CCC1=NC(C2=CC=C(OCC)C=C2)=NO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 1, 1, 8, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [121, 121, 121, 74, 58, 58, 28, 58, 19, 4, 4, 4, 1, 1, 1, 1, 1, 1, 6, 14, 1, 1, 4, 4, 74, 95, 95, 121, 121, 121, 121, 121, 74, 58, 28, 28, 19, 19, 1, 1, 14, 14, 15, 15, 15, 1, 1] 201 rigid atoms, others: [45, 38, 39, 46, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 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: 624 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919128 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919128 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919128/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919128 Building REAL300004919129 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919129' /scratch/stefan/7775247/working/building/REAL300004919129 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919129 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919129/0 /scratch/stefan/7775247/working/building/REAL300004919129 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 129) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/129 `/scratch/stefan/7775247/working/3D/129' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C1=CC=CC=C1)N1C=CC=N1)C(=O)[O-]) `REAL300004919129.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919129 none CC#CCC(NC(=O)C(C1=CC=CC=C1)N1C=CC=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 49, 20, 20, 4, 20, 1, 1, 1, 1, 1, 1, 1, 4, 19, 19, 19, 19, 49, 75, 75, 107, 107, 107, 107, 107, 49, 20, 4, 1, 1, 1, 1, 1, 19, 19, 19] 140 rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919129 none CC#CCC(NC(=O)C(C1=CC=CC=C1)N1C=CC=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [138, 138, 138, 73, 41, 41, 13, 41, 1, 13, 19, 19, 16, 19, 19, 1, 1, 1, 1, 1, 73, 105, 105, 138, 138, 138, 138, 138, 73, 41, 13, 19, 19, 19, 19, 19, 1, 1, 1] 140 rigid atoms, others: [36, 37, 38, 8, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 729 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919129 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919129 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919129/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919129 Building REAL300004919130 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919130' /scratch/stefan/7775247/working/building/REAL300004919130 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919130 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919130/0 /scratch/stefan/7775247/working/building/REAL300004919130 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/130 `/scratch/stefan/7775247/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC(Br)=C2)N=N1)C(=O)[O-]) `REAL300004919130.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919130 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC(Br)=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 17, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 31, 10, 10, 1, 10, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 31, 41, 41, 55, 55, 55, 55, 55, 31, 10, 2, 2, 2, 5, 5, 5, 5] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 276 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919130 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC(Br)=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 17, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 113, 38, 38, 5, 38, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 113, 152, 152, 201, 201, 201, 201, 201, 113, 38, 5, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 998 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919130 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919130 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919130/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919130 Building REAL300004919131 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919131' /scratch/stefan/7775247/working/building/REAL300004919131 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919131 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919131/0 /scratch/stefan/7775247/working/building/REAL300004919131 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/131 `/scratch/stefan/7775247/working/3D/131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(N2C(=O)NC=C2C)C=C1)C(=O)[O-]) `REAL300004919131.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919131 none CC#CCC(NC(=O)C1=CC=C(N2C(=O)NC=C2C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 5, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 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: [44, 44, 44, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1, 15, 22, 22, 44, 44, 44, 44, 44, 15, 4, 1, 1, 9, 9, 9, 9, 9, 1, 1] 125 rigid atoms, others: [32, 38, 6, 39, 8, 9, 10, 11, 12, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 205 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: REAL300004919131 none CC#CCC(NC(=O)C1=CC=C(N2C(=O)NC=C2C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 5, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 125, 57, 21, 21, 1, 21, 1, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 57, 79, 79, 125, 125, 125, 125, 125, 57, 21, 9, 9, 1, 1, 2, 2, 2, 9, 9] 125 rigid atoms, others: [33, 34, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 612 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919131 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919131 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919131/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919131 Building REAL300004919132 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919132' /scratch/stefan/7775247/working/building/REAL300004919132 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919132 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919132/0 /scratch/stefan/7775247/working/building/REAL300004919132 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/132 `/scratch/stefan/7775247/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=NC(=O)C2=C(N1)SC(C)=C2C)C(=O)[O-]) `REAL300004919132.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919132 none CC#CCC(NC(=O)CCC1=NC(=O)C2=C(N1)SC(C)=C2C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'S.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 5, 1, 8, 1, 11, 1, 1, 8, 14, 1, 5, 1, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 11, 9, 9, 5, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 17, 17, 17, 17, 17, 11, 9, 5, 5, 5, 5, 1, 2, 2, 2, 2, 2, 2] 17 rigid atoms, others: [36, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 82 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919132 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919132 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919132/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919132 Building REAL300004919133 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919133' /scratch/stefan/7775247/working/building/REAL300004919133 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919133 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919133/0 /scratch/stefan/7775247/working/building/REAL300004919133 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 133) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/133 `/scratch/stefan/7775247/working/3D/133' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(Br)C=C1OC(C)C)C(=O)[O-]) `REAL300004919133.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919133 none CC#CCC(NC(=O)C1=CC=C(Br)C=C1OC(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 17, 1, 1, 12, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 37, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 9, 19, 19, 37, 62, 62, 112, 112, 112, 112, 112, 37, 12, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 599 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919133 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919133 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919133/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919133 Building REAL300004919134 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919134' /scratch/stefan/7775247/working/building/REAL300004919134 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919134 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919134/0 /scratch/stefan/7775247/working/building/REAL300004919134 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/134 `/scratch/stefan/7775247/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(CCOC)C2=CC=CC=C12)C(=O)[O-]) `REAL300004919134.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919134 none CC#CCC(NC(=O)C1=CN(CCOC)C2=CC=CC=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 8, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 27, 9, 9, 1, 9, 1, 1, 1, 1, 6, 11, 24, 1, 1, 1, 1, 1, 1, 27, 40, 40, 69, 69, 69, 69, 69, 27, 9, 1, 6, 6, 11, 11, 24, 24, 24, 1, 1, 1, 1] 201 rigid atoms, others: [6, 39, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 41, 40, 42, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 378 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919134 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919134 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919134/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919134 Building REAL300004919135 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919135' /scratch/stefan/7775247/working/building/REAL300004919135 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919135 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919135/0 /scratch/stefan/7775247/working/building/REAL300004919135 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 135) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/135 `/scratch/stefan/7775247/working/3D/135' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCN1C(=O)C(C)(C)C)C(=O)[O-]) `REAL300004919135.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919135 none CC#CCC(NC(=O)C1CCCN1C(=O)C(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 15, 22, 22, 30, 30, 30, 30, 30, 15, 7, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4] 35 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 160 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919135 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919135 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919135/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919135 Building REAL300004919136 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919136' /scratch/stefan/7775247/working/building/REAL300004919136 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919136 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919136/0 /scratch/stefan/7775247/working/building/REAL300004919136 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/136 `/scratch/stefan/7775247/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CSC2(C)CCC(=O)N12)C(=O)[O-]) `REAL300004919136.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919136 none CC#CCC(NC(=O)C1CSC2(C)CCC(=O)N12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 14, 5, 5, 5, 5, 1, 11, 8, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 2, 2, 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: [74, 74, 74, 36, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 51, 51, 74, 74, 74, 74, 74, 36, 11, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1] 74 rigid atoms, others: [34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 32, 33, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31]) total number of confs: 359 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919136 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919136 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919136/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919136 Building REAL300004919137 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919137' /scratch/stefan/7775247/working/building/REAL300004919137 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919137 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919137/0 /scratch/stefan/7775247/working/building/REAL300004919137 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 137) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/137 `/scratch/stefan/7775247/working/3D/137' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(SCC1=CC=CC=C1)C(C)C)C(=O)[O-]) `REAL300004919137.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919137 none CC#CCC(NC(=O)C(SCC1=CC=CC=C1)C(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 14, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 126, 75, 75, 48, 75, 15, 4, 1, 1, 1, 1, 1, 1, 1, 48, 53, 53, 126, 164, 164, 201, 201, 201, 201, 201, 126, 75, 48, 4, 4, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53, 53] 201 rigid atoms, others: [33, 34, 35, 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, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 1060 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919137 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919137 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919137/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919137 Building REAL300004919138 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919138' /scratch/stefan/7775247/working/building/REAL300004919138 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919138 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919138/0 /scratch/stefan/7775247/working/building/REAL300004919138 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/138 `/scratch/stefan/7775247/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C2=CC=CO2)=NC2=CC=CC=C21)C(=O)[O-]) `REAL300004919138.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919138 none CC#CCC(NC(=O)C1=CC(C2=CC=CO2)=NC2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 32, 9, 9, 1, 9, 1, 1, 1, 1, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 32, 50, 50, 90, 90, 90, 90, 90, 32, 9, 1, 12, 12, 12, 1, 1, 1, 1] 201 rigid atoms, others: [33, 37, 6, 39, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36]) total number of confs: 442 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919138 none CC#CCC(NC(=O)C1=CC(C2=CC=CO2)=NC2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 125, 66, 66, 12, 66, 12, 12, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 11, 11, 125, 152, 152, 201, 201, 201, 201, 201, 125, 66, 12, 1, 1, 1, 12, 12, 12, 12] 201 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 906 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919138 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919138 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919138/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919138 Building REAL300004919139 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919139' /scratch/stefan/7775247/working/building/REAL300004919139 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919139 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919139/0 /scratch/stefan/7775247/working/building/REAL300004919139 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 139) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/139 `/scratch/stefan/7775247/working/3D/139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(Br)C(F)=C1)C(=O)[O-]) `REAL300004919139.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919139 none CC#CCC(NC(=O)C1=CC=C(Br)C(F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 17, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 29, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 29, 40, 40, 66, 66, 66, 66, 66, 29, 7, 1, 1, 1] 66 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 302 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919139 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919139 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919139/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919139 Building REAL300004919140 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919140' /scratch/stefan/7775247/working/building/REAL300004919140 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919140 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919140/0 /scratch/stefan/7775247/working/building/REAL300004919140 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/140 `/scratch/stefan/7775247/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=CC(F)=C2)C(C(C)C)=N1)C(=O)[O-]) `REAL300004919140.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919140 none CC#CCC(NC(=O)C1=NN(C2=CC=CC(F)=C2)C(C(C)C)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 6, 6, 1, 6, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 6, 6, 1, 21, 33, 33, 64, 64, 64, 64, 64, 21, 6, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6] 201 rigid atoms, others: [6, 8, 9, 10, 11, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 324 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919140 none CC#CCC(NC(=O)C1=NN(C2=CC=CC(F)=C2)C(C(C)C)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 198, 77, 25, 25, 5, 25, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 13, 5, 77, 119, 119, 198, 198, 198, 198, 198, 77, 25, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 999 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919140 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919140 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919140/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919140 Building REAL300004919141 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919141' /scratch/stefan/7775247/working/building/REAL300004919141 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919141 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919141/0 /scratch/stefan/7775247/working/building/REAL300004919141 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 141) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/141 `/scratch/stefan/7775247/working/3D/141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC)C=C1Br)C(=O)[O-]) `REAL300004919141.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919141 none CC#CCC(NC(=O)C1=CC=C(OC)C=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 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: [62, 62, 62, 22, 7, 7, 1, 7, 1, 1, 1, 1, 1, 2, 1, 1, 1, 22, 33, 33, 62, 62, 62, 62, 62, 22, 7, 1, 1, 3, 3, 3, 1] 107 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 14, 15, 16, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 292 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919141 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919141 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919141/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919141 Building REAL300004919142 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919142' /scratch/stefan/7775247/working/building/REAL300004919142 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919142 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919142/0 /scratch/stefan/7775247/working/building/REAL300004919142 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/142 `/scratch/stefan/7775247/working/3D/142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(C2=CC=CC=C2)N=C1C(C)(C)C)C(=O)[O-]) `REAL300004919142.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919142 none CC#CCC(NC(=O)C1=CN(C2=CC=CC=C2)N=C1C(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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: [56, 56, 56, 22, 6, 6, 1, 6, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 1, 4, 4, 4, 22, 35, 35, 56, 56, 56, 56, 56, 22, 6, 1, 4, 4, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 59 rigid atoms, others: [33, 6, 8, 9, 10, 11, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 296 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919142 none CC#CCC(NC(=O)C1=CN(C2=CC=CC=C2)N=C1C(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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: [58, 58, 58, 32, 13, 13, 4, 13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 32, 42, 42, 58, 58, 58, 58, 58, 32, 13, 4, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8] 59 rigid atoms, others: [34, 35, 36, 37, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 294 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919142 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919142 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919142/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919142 Building REAL300004919143 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919143' /scratch/stefan/7775247/working/building/REAL300004919143 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919143 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919143/0 /scratch/stefan/7775247/working/building/REAL300004919143 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/143 `/scratch/stefan/7775247/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)(C)C1=CC=C(OC)C(OC)=C1)C(=O)[O-]) `REAL300004919143.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919143 none CC#CCC(NC(=O)C(C)(C)C1=CC=C(OC)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 55, 27, 27, 13, 27, 1, 13, 13, 1, 1, 1, 1, 1, 3, 1, 1, 3, 1, 55, 82, 82, 114, 114, 114, 114, 114, 55, 27, 13, 13, 13, 13, 13, 13, 1, 1, 4, 4, 4, 4, 4, 4, 1] 201 rigid atoms, others: [45, 37, 38, 8, 11, 12, 13, 14, 15, 17, 18, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 16, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 615 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919143 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919143 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919143/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919143 Building REAL300004919144 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919144' /scratch/stefan/7775247/working/building/REAL300004919144 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919144 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919144/0 /scratch/stefan/7775247/working/building/REAL300004919144 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/144 `/scratch/stefan/7775247/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)(C)C1=CC=CC=C1OC)C(=O)[O-]) `REAL300004919144.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919144 none CC#CCC(NC(=O)C(C)(C)C1=CC=CC=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 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: [104, 104, 104, 45, 19, 19, 5, 19, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 45, 67, 67, 104, 104, 104, 104, 104, 45, 19, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2] 104 rigid atoms, others: [35, 36, 37, 38, 8, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41]) total number of confs: 521 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919144 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919144 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919144/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919144 Building REAL300004919145 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919145' /scratch/stefan/7775247/working/building/REAL300004919145 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919145 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919145/0 /scratch/stefan/7775247/working/building/REAL300004919145 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 145) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/145 `/scratch/stefan/7775247/working/3D/145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCC1=C(C)SC(C)=C1)C(=O)[O-]) `REAL300004919145.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919145 none CC#CCC(NC(=O)CCCC1=C(C)SC(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 1, 1, 5, 14, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 102, 53, 53, 13, 53, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 102, 144, 144, 201, 201, 201, 201, 201, 102, 53, 13, 13, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 1] 201 rigid atoms, others: [40, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 1057 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919145 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919145 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919145/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919145 Building REAL300004919146 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919146' /scratch/stefan/7775247/working/building/REAL300004919146 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919146 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919146/0 /scratch/stefan/7775247/working/building/REAL300004919146 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/146 `/scratch/stefan/7775247/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCCN1S(=O)(=O)C1=CC=CS1)C(=O)[O-]) `REAL300004919146.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919146 none CC#CCC(NC(=O)C1CCCCN1S(=O)(=O)C1=CC=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 11, 16, 16, 28, 28, 28, 28, 28, 11, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8] 44 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43]) total number of confs: 152 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: REAL300004919146 none CC#CCC(NC(=O)C1CCCCN1S(=O)(=O)C1=CC=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 21, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 1, 6, 6, 1, 1, 1, 1, 1, 21, 27, 27, 44, 44, 44, 44, 44, 21, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1] 44 rigid atoms, others: [41, 42, 43, 14, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 215 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919146 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919146 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919146/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919146 Building REAL300004919147 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919147' /scratch/stefan/7775247/working/building/REAL300004919147 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919147 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919147/0 /scratch/stefan/7775247/working/building/REAL300004919147 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 147) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/147 `/scratch/stefan/7775247/working/3D/147' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CC2=CC=C(C)C=C2S1)C(=O)[O-]) `REAL300004919147.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919147 none CC#CCC(NC(=O)C1CC2=CC=C(C)C=C2S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 1, 1, 1, 1, 5, 1, 1, 14, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 39, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 54, 54, 82, 82, 82, 82, 82, 39, 12, 1, 1, 1, 1, 1, 2, 2, 2, 1] 82 rigid atoms, others: [32, 36, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 35, 7, 34, 33, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 388 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919147 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919147 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919147/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919147 Building REAL300004919148 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919148' /scratch/stefan/7775247/working/building/REAL300004919148 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919148 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919148/0 /scratch/stefan/7775247/working/building/REAL300004919148 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/148 `/scratch/stefan/7775247/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=CC(Br)=CC=C2OC1)C(=O)[O-]) `REAL300004919148.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919148 none CC#CCC(NC(=O)C1=CC2=CC(Br)=CC=C2OC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 17, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 38, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 54, 54, 88, 88, 88, 88, 88, 38, 12, 1, 1, 1, 1, 1, 1] 88 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 419 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919148 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919148 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919148/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919148 Building REAL300004919149 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919149' /scratch/stefan/7775247/working/building/REAL300004919149 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919149 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919149/0 /scratch/stefan/7775247/working/building/REAL300004919149 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/149 `/scratch/stefan/7775247/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(OC)=CC(Br)=C1OC)C(=O)[O-]) `REAL300004919149.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919149 none CC#CCC(NC(=O)C1=CC(OC)=CC(Br)=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 12, 5, 1, 1, 17, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 35, 13, 12, 1, 12, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 2, 35, 58, 58, 102, 102, 102, 102, 102, 35, 13, 1, 3, 3, 3, 1, 2, 2, 2] 201 rigid atoms, others: [33, 6, 8, 9, 10, 11, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 7, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 34, 35, 36]) total number of confs: 489 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919149 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919149 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919149/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919149 Building REAL300004919150 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919150' /scratch/stefan/7775247/working/building/REAL300004919150 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919150 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919150/0 /scratch/stefan/7775247/working/building/REAL300004919150 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/150 `/scratch/stefan/7775247/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)N(C)C)=C1)C(=O)[O-]) `REAL300004919150.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919150 none CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)N(C)C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 9, 9, 9, 14, 14, 1, 17, 31, 31, 59, 59, 59, 59, 59, 17, 5, 1, 1, 1, 14, 14, 14, 14, 14, 14, 1] 201 rigid atoms, others: [32, 6, 39, 8, 9, 10, 11, 12, 13, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 327 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919150 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919150 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919150/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919150 Building REAL300004919151 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919151' /scratch/stefan/7775247/working/building/REAL300004919151 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919151 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919151/0 /scratch/stefan/7775247/working/building/REAL300004919151 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 151) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/151 `/scratch/stefan/7775247/working/3D/151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC12CC3CC(CC(C3)C1)C2)C(=O)[O-]) `REAL300004919151.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919151 none CC#CCC(NC(=O)CC12CC3CC(CC(C3)C1)C2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 34, 14, 13, 3, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 46, 46, 68, 68, 68, 68, 68, 34, 14, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 68 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 331 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919151 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919151 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919151/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919151 Building REAL300004919152 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919152' /scratch/stefan/7775247/working/building/REAL300004919152 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919152 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919152/0 /scratch/stefan/7775247/working/building/REAL300004919152 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/152 `/scratch/stefan/7775247/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)N2CCOCC2)=C1)C(=O)[O-]) `REAL300004919152.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919152 none CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)N2CCOCC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 16, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 23, 23, 23, 23, 23, 1, 16, 24, 24, 41, 41, 41, 41, 41, 16, 5, 1, 1, 1, 23, 23, 24, 24, 24, 24, 23, 23, 1] 201 rigid atoms, others: [33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 44, 22] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43]) 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: REAL300004919152 none CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)N2CCOCC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 125, 67, 67, 24, 67, 24, 24, 24, 24, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 24, 125, 161, 161, 201, 201, 201, 201, 201, 125, 67, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 24] 201 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 13, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44]) total number of confs: 954 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919152 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919152 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919152/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919152 Building REAL300004919153 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919153' /scratch/stefan/7775247/working/building/REAL300004919153 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919153 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919153/0 /scratch/stefan/7775247/working/building/REAL300004919153 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/153 `/scratch/stefan/7775247/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC(OC)=C(OC)C(OC)=C1)C(=O)[O-]) `REAL300004919153.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919153 none CC#CCC(NC(=O)CCC1=CC(OC)=C(OC)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 1, 1, 1, 12, 5, 1, 12, 5, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 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: [12, 12, 12, 7, 5, 5, 4, 5, 3, 1, 1, 1, 1, 1, 3, 1, 1, 6, 1, 1, 3, 1, 7, 10, 10, 12, 12, 12, 12, 12, 7, 5, 4, 4, 3, 3, 1, 3, 3, 3, 6, 6, 6, 3, 3, 3, 1] 16 rigid atoms, others: [36, 9, 10, 11, 12, 13, 46, 15, 16, 18, 19, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 17, 20, 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: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919153 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919153 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919153/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919153 Building REAL300004919154 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919154' /scratch/stefan/7775247/working/building/REAL300004919154 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919154 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919154/0 /scratch/stefan/7775247/working/building/REAL300004919154 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/154 `/scratch/stefan/7775247/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=CC=CC=C2C=C1OC)C(=O)[O-]) `REAL300004919154.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919154 none CC#CCC(NC(=O)C1=CC2=CC=CC=C2C=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 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: [115, 115, 115, 47, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 47, 71, 71, 115, 115, 115, 115, 115, 47, 12, 1, 1, 1, 1, 1, 1, 3, 3, 3] 124 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 38, 7, 37, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36]) total number of confs: 547 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919154 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919154 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919154/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919154 Building REAL300004919155 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919155' /scratch/stefan/7775247/working/building/REAL300004919155 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919155 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919155/0 /scratch/stefan/7775247/working/building/REAL300004919155 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/155 `/scratch/stefan/7775247/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(N2CCC(C)CC2)C([N+](=O)[O-])=C1)C(=O)[O-]) `REAL300004919155.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919155 none CC#CCC(NC(=O)C1=CC=C(N2CCC(C)CC2)C([N+](=O)[O-])=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 5, 1, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 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: [67, 67, 67, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 2, 2, 1, 27, 40, 40, 67, 67, 67, 67, 67, 27, 7, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1] 68 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 48, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 321 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919155 none CC#CCC(NC(=O)C1=CC=C(N2CCC(C)CC2)C([N+](=O)[O-])=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 5, 1, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 36, 13, 13, 1, 13, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 36, 47, 47, 68, 68, 68, 68, 68, 36, 13, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 4] 68 rigid atoms, others: [45, 36, 37, 39, 44, 47, 11, 12, 13, 14, 15, 16, 17, 18, 46, 40, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 48]) total number of confs: 338 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919155 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919155 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919155/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919155 Building REAL300004919156 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919156' /scratch/stefan/7775247/working/building/REAL300004919156 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919156 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919156/0 /scratch/stefan/7775247/working/building/REAL300004919156 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/156 `/scratch/stefan/7775247/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(N2CC(C)CC(C)C2)C([N+](=O)[O-])=C1)C(=O)[O-]) `REAL300004919156.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919156 none CC#CCC(NC(=O)C1=CC=C(N2CC(C)CC(C)C2)C([N+](=O)[O-])=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 5, 5, 1, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 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: [67, 67, 67, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 1, 1, 2, 2, 1, 26, 43, 43, 67, 67, 67, 67, 67, 26, 7, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1] 90 rigid atoms, others: [35, 36, 6, 8, 9, 10, 11, 12, 51, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 340 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919156 none CC#CCC(NC(=O)C1=CC=C(N2CC(C)CC(C)C2)C([N+](=O)[O-])=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 5, 5, 1, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 47, 15, 15, 1, 15, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 47, 64, 64, 90, 90, 90, 90, 90, 47, 15, 4, 4, 1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2, 1, 1, 4] 90 rigid atoms, others: [45, 43, 37, 39, 44, 11, 12, 13, 14, 15, 16, 17, 18, 19, 50, 49, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 46, 47, 48, 51]) total number of confs: 456 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919156 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919156 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919156/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919156 Building REAL300004919157 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919157' /scratch/stefan/7775247/working/building/REAL300004919157 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919157 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919157/0 /scratch/stefan/7775247/working/building/REAL300004919157 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 157) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/157 `/scratch/stefan/7775247/working/3D/157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC)C(S(=O)(=O)N2CCCC2)=C1)C(=O)[O-]) `REAL300004919157.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919157 none CC#CCC(NC(=O)C1=CC=C(OC)C(S(=O)(=O)N2CCCC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 3, 1, 1, 9, 9, 9, 21, 21, 21, 21, 1, 17, 29, 29, 59, 59, 59, 59, 59, 17, 5, 1, 1, 4, 4, 4, 21, 21, 21, 21, 21, 21, 21, 21, 1] 201 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 14, 15, 23, 47] set([0, 1, 2, 3, 4, 5, 7, 13, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 327 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919157 none CC#CCC(NC(=O)C1=CC=C(OC)C(S(=O)(=O)N2CCCC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [175, 175, 175, 108, 52, 52, 21, 52, 21, 21, 21, 21, 21, 28, 5, 1, 5, 5, 1, 1, 1, 1, 1, 21, 108, 145, 145, 175, 175, 175, 175, 175, 108, 52, 21, 21, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 21] 201 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 47]) total number of confs: 885 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919157 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919157 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919157/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919157 Building REAL300004919158 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919158' /scratch/stefan/7775247/working/building/REAL300004919158 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919158 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919158/0 /scratch/stefan/7775247/working/building/REAL300004919158 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/158 `/scratch/stefan/7775247/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCOC1=CC=C(Cl)C(C)=C1)C(=O)[O-]) `REAL300004919158.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919158 none CC#CCC(NC(=O)CCCOC1=CC=C(Cl)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 122, 93, 93, 38, 93, 28, 10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 122, 156, 156, 201, 201, 201, 201, 201, 122, 93, 38, 38, 28, 28, 10, 10, 1, 1, 2, 2, 2, 1] 201 rigid atoms, others: [36, 37, 41, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 1082 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919158 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919158 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919158/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919158 Building REAL300004919159 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919159' /scratch/stefan/7775247/working/building/REAL300004919159 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919159 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919159/0 /scratch/stefan/7775247/working/building/REAL300004919159 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 159) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/159 `/scratch/stefan/7775247/working/3D/159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C1=CC=C(Cl)C=C1)C(C)C)C(=O)[O-]) `REAL300004919159.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919159 none CC#CCC(NC(=O)C(C1=CC=C(Cl)C=C1)C(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 40, 14, 14, 4, 14, 1, 1, 1, 1, 1, 1, 1, 1, 4, 6, 6, 40, 61, 61, 114, 114, 114, 114, 114, 40, 14, 4, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6] 133 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 540 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919159 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919159 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919159/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919159 Building REAL300004919160 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919160' /scratch/stefan/7775247/working/building/REAL300004919160 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919160 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919160/0 /scratch/stefan/7775247/working/building/REAL300004919160 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/160 `/scratch/stefan/7775247/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCOC1=CC=C(C(C)(C)C)C=C1)C(=O)[O-]) `REAL300004919160.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919160 none CC#CCC(NC(=O)CCCOC1=CC=C(C(C)(C)C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [199, 199, 199, 134, 95, 95, 29, 95, 16, 6, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 134, 137, 137, 199, 199, 199, 199, 199, 134, 95, 29, 29, 16, 16, 6, 6, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1] 201 rigid atoms, others: [38, 39, 11, 12, 13, 14, 15, 16, 49, 50, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 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]) total number of confs: 929 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919160 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919160 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919160/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919160 Building REAL300004919161 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919161' /scratch/stefan/7775247/working/building/REAL300004919161 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919161 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919161/0 /scratch/stefan/7775247/working/building/REAL300004919161 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 161) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/161 `/scratch/stefan/7775247/working/3D/161' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OCC(C)C)C=C1)C(=O)[O-]) `REAL300004919161.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919161 none CC#CCC(NC(=O)C1=CC=C(OCC(C)C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 7, 19, 25, 33, 1, 1, 9, 15, 15, 34, 34, 34, 34, 34, 9, 3, 1, 1, 19, 19, 33, 33, 33, 33, 33, 33, 33, 1, 1] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 17, 18, 41, 40, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 334 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919161 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919161 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919161/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919161 Building REAL300004919162 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919162' /scratch/stefan/7775247/working/building/REAL300004919162 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919162 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919162/0 /scratch/stefan/7775247/working/building/REAL300004919162 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/162 `/scratch/stefan/7775247/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OCC(C)C)C(OC)=C1)C(=O)[O-]) `REAL300004919162.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919162 none CC#CCC(NC(=O)C1=CC=C(OCC(C)C)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 9, 17, 22, 24, 1, 1, 3, 1, 11, 17, 17, 30, 30, 30, 30, 30, 11, 5, 1, 1, 17, 17, 24, 24, 24, 24, 24, 24, 24, 3, 3, 3, 1] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 45, 17, 18, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919162 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919162 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919162/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919162 Building REAL300004919163 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919163' /scratch/stefan/7775247/working/building/REAL300004919163 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919163 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919163/0 /scratch/stefan/7775247/working/building/REAL300004919163 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/163 `/scratch/stefan/7775247/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCN1C(=O)OC(C)(C)C)C(=O)[O-]) `REAL300004919163.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919163 none CC#CCC(NC(=O)C1CCCN1C(=O)OC(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [76, 76, 76, 26, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 5, 5, 15, 17, 17, 17, 26, 42, 42, 76, 76, 76, 76, 76, 26, 10, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18] 178 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 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]) total number of confs: 412 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919163 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919163 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919163/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919163 Building REAL300004919164 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919164' /scratch/stefan/7775247/working/building/REAL300004919164 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919164 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919164/0 /scratch/stefan/7775247/working/building/REAL300004919164 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/164 `/scratch/stefan/7775247/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)C2=CC(Br)=CC=C2O1)C(=O)[O-]) `REAL300004919164.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919164 none CC#CCC(NC(=O)C1=C(C)C2=CC(Br)=CC=C2O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 1, 1, 1, 17, 1, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 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: [59, 59, 59, 31, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 40, 40, 59, 59, 59, 59, 59, 31, 11, 2, 2, 2, 1, 1, 1] 59 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 275 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919164 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919164 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919164/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919164 Building REAL300004919165 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919165' /scratch/stefan/7775247/working/building/REAL300004919165 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919165 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919165/0 /scratch/stefan/7775247/working/building/REAL300004919165 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/165 `/scratch/stefan/7775247/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC=CC2=CC=CC=C21)C(=O)[O-]) `REAL300004919165.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919165 none CC#CCC(NC(=O)COC1=CC=CC2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 184, 140, 140, 33, 140, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 184, 184, 184, 201, 201, 201, 201, 201, 184, 140, 33, 33, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 738 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919165 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919165 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919165/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919165 Building REAL300004919166 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919166' /scratch/stefan/7775247/working/building/REAL300004919166 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919166 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919166/0 /scratch/stefan/7775247/working/building/REAL300004919166 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/166 `/scratch/stefan/7775247/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Br)=C(Br)S1)C(=O)[O-]) `REAL300004919166.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919166 none CC#CCC(NC(=O)C1=CC(Br)=C(Br)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'Br', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 17, 1, 17, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 34, 10, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 34, 47, 47, 66, 66, 66, 66, 66, 34, 11, 1] 66 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 25] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 334 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919166 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919166 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919166/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919166 Building REAL300004919167 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919167' /scratch/stefan/7775247/working/building/REAL300004919167 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919167 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919167/0 /scratch/stefan/7775247/working/building/REAL300004919167 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/167 `/scratch/stefan/7775247/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)C2=CC(OCC)=CC=C2O1)C(=O)[O-]) `REAL300004919167.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919167 none CC#CCC(NC(=O)C1=C(C)C2=CC(OCC)=CC=C2O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 5, 1, 1, 1, 12, 5, 5, 1, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 98, 39, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 18, 1, 1, 1, 1, 39, 64, 64, 98, 98, 98, 98, 98, 39, 12, 2, 2, 2, 1, 18, 18, 19, 19, 19, 1, 1] 201 rigid atoms, others: [34, 6, 8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 20, 41, 40] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39]) total number of confs: 556 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919167 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919167 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919167/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919167 Building REAL300004919168 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919168' /scratch/stefan/7775247/working/building/REAL300004919168 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919168 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919168/0 /scratch/stefan/7775247/working/building/REAL300004919168 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/168 `/scratch/stefan/7775247/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=COC2=CC(CC)=CC=C12)C(=O)[O-]) `REAL300004919168.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919168 none CC#CCC(NC(=O)CC1=COC2=CC(CC)=CC=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 1, 1, 12, 1, 1, 1, 5, 5, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 52, 34, 34, 8, 34, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 52, 76, 76, 108, 108, 108, 108, 108, 52, 34, 8, 8, 1, 1, 2, 2, 3, 3, 3, 1, 1] 201 rigid atoms, others: [32, 33, 39, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 559 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919168 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919168 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919168/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919168 Building REAL300004919169 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919169' /scratch/stefan/7775247/working/building/REAL300004919169 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919169 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919169/0 /scratch/stefan/7775247/working/building/REAL300004919169 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/169 `/scratch/stefan/7775247/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC=CC=C1C(C)C)C(=O)[O-]) `REAL300004919169.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919169 none CC#CCC(NC(=O)COC1=CC=CC=C1C(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 134, 96, 96, 26, 96, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 134, 167, 167, 201, 201, 201, 201, 201, 134, 96, 26, 26, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 968 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919169 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919169 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919169/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919169 Building REAL300004919170 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919170' /scratch/stefan/7775247/working/building/REAL300004919170 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919170 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919170/0 /scratch/stefan/7775247/working/building/REAL300004919170 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/170 `/scratch/stefan/7775247/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OCCC)C(OCC)=C1)C(=O)[O-]) `REAL300004919170.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919170 none CC#CCC(NC(=O)C1=CC=C(OCCC)C(OCC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 5, 1, 12, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 9, 26, 43, 1, 1, 9, 15, 1, 9, 13, 13, 25, 25, 25, 25, 25, 9, 5, 1, 1, 26, 26, 46, 46, 46, 46, 46, 15, 15, 16, 16, 16, 1] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 45, 16, 17, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 361 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919170 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919170 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919170/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919170 Building REAL300004919171 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919171' /scratch/stefan/7775247/working/building/REAL300004919171 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919171 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919171/0 /scratch/stefan/7775247/working/building/REAL300004919171 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 171) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/171 `/scratch/stefan/7775247/working/3D/171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CSC1=CC=C(C)C=C1C)C(=O)[O-]) `REAL300004919171.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919171 none CC#CCC(NC(=O)CSC1=CC=C(C)C=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 14, 1, 1, 1, 1, 5, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 134, 134, 30, 134, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 182, 186, 186, 201, 201, 201, 201, 201, 182, 134, 30, 30, 1, 1, 2, 2, 2, 1, 2, 2, 2] 201 rigid atoms, others: [35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 36, 37, 38]) total number of confs: 773 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919171 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919171 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919171/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919171 Building REAL300004919172 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919172' /scratch/stefan/7775247/working/building/REAL300004919172 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919172 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919172/0 /scratch/stefan/7775247/working/building/REAL300004919172 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/172 `/scratch/stefan/7775247/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=C(C)C=C(Br)C=C1Cl)C(=O)[O-]) `REAL300004919172.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919172 none CC#CCC(NC(=O)COC1=C(C)C=C(Br)C=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 1, 1, 17, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 124, 70, 70, 9, 70, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 124, 166, 166, 201, 201, 201, 201, 201, 124, 70, 9, 9, 2, 2, 2, 1, 1] 201 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 1020 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919172 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919172 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919172/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919172 Building REAL300004919173 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919173' /scratch/stefan/7775247/working/building/REAL300004919173 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919173 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919173/0 /scratch/stefan/7775247/working/building/REAL300004919173 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/173 `/scratch/stefan/7775247/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C12CC3CC(C)(CC(C)(C3)C1)C2)C(=O)[O-]) `REAL300004919173.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919173 none CC#CCC(NC(=O)C12CC3CC(C)(CC(C)(C3)C1)C2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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, 31, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 46, 46, 82, 82, 82, 82, 82, 31, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1] 82 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 5, 7, 40, 41, 42, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 383 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919173 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919173 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919173/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919173 Building REAL300004919174 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919174' /scratch/stefan/7775247/working/building/REAL300004919174 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919174 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919174/0 /scratch/stefan/7775247/working/building/REAL300004919174 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/174 `/scratch/stefan/7775247/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(SC)C([N+](=O)[O-])=C1)C(=O)[O-]) `REAL300004919174.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919174 none CC#CCC(NC(=O)C1=CC=C(SC)C([N+](=O)[O-])=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 5, 1, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 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: [104, 104, 104, 30, 7, 7, 1, 7, 1, 1, 1, 1, 1, 7, 1, 1, 2, 2, 1, 30, 48, 48, 104, 104, 104, 104, 104, 30, 7, 1, 1, 7, 7, 7, 1] 187 rigid atoms, others: [34, 6, 8, 9, 10, 11, 12, 14, 15, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33]) total number of confs: 464 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919174 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919174 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919174/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919174 Building REAL300004919175 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919175' /scratch/stefan/7775247/working/building/REAL300004919175 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919175 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919175/0 /scratch/stefan/7775247/working/building/REAL300004919175 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/175 `/scratch/stefan/7775247/working/3D/175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCNC1=NS(=O)(=O)C2=CC=CC=C21)C(=O)[O-]) `REAL300004919175.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919175 none CC#CCC(NC(=O)CCCNC1=NS(=O)(=O)C2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 5, 5, 8, 1, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 33, 31, 31, 23, 31, 20, 18, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 35, 35, 35, 35, 35, 33, 31, 22, 23, 21, 21, 18, 18, 3, 1, 1, 1, 1] 35 rigid atoms, others: [43, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919175 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919175 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919175/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919175 Building REAL300004919176 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919176' /scratch/stefan/7775247/working/building/REAL300004919176 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919176 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919176/0 /scratch/stefan/7775247/working/building/REAL300004919176 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/176 `/scratch/stefan/7775247/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)C(F)F)C=C1)C(=O)[O-]) `REAL300004919176.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919176 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)C(F)F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 5, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 2, 2, 2, 18, 18, 1, 1, 16, 26, 26, 64, 64, 64, 64, 64, 16, 4, 1, 1, 18, 1, 1] 192 rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 12, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32]) total number of confs: 334 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919176 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919176 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919176/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919176 Building REAL300004919177 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919177' /scratch/stefan/7775247/working/building/REAL300004919177 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919177 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919177/0 /scratch/stefan/7775247/working/building/REAL300004919177 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/177 `/scratch/stefan/7775247/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CSCC1=CC=C(F)C=C1)C(=O)[O-]) `REAL300004919177.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919177 none CC#CCC(NC(=O)CSCC1=CC=C(F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 146, 146, 63, 146, 17, 3, 1, 1, 1, 1, 1, 1, 1, 1, 180, 183, 183, 201, 201, 201, 201, 201, 180, 146, 63, 63, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 795 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919177 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919177 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919177/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919177 Building REAL300004919178 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919178' /scratch/stefan/7775247/working/building/REAL300004919178 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919178 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919178/0 /scratch/stefan/7775247/working/building/REAL300004919178 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/178 `/scratch/stefan/7775247/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=CC=C(Cl)C=C2)N=C1)C(=O)[O-]) `REAL300004919178.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919178 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=C(Cl)C=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 16, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [122, 122, 122, 51, 12, 12, 1, 12, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 51, 77, 77, 122, 122, 122, 122, 122, 51, 12, 2, 2, 2, 4, 4, 4, 4, 1] 149 rigid atoms, others: [38, 6, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 595 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919178 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=C(Cl)C=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 16, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [149, 149, 149, 82, 26, 26, 4, 26, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 82, 107, 107, 149, 149, 149, 149, 149, 82, 26, 4, 4, 4, 1, 1, 1, 1, 4] 149 rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 690 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919178 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919178 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919178/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919178 Building REAL300004919179 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919179' /scratch/stefan/7775247/working/building/REAL300004919179 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919179 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919179/0 /scratch/stefan/7775247/working/building/REAL300004919179 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/179 `/scratch/stefan/7775247/working/3D/179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=C(Cl)C=C2)C(C2=CC=CO2)=C1)C(=O)[O-]) `REAL300004919179.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919179 none CC#CCC(NC(=O)C1=NN(C2=CC=C(Cl)C=C2)C(C2=CC=CO2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 8, 8, 1, 8, 1, 1, 1, 1, 5, 5, 2, 3, 5, 5, 1, 1, 12, 12, 12, 12, 1, 22, 35, 35, 64, 64, 64, 64, 64, 22, 8, 5, 5, 5, 5, 12, 12, 12, 1] 201 rigid atoms, others: [6, 8, 9, 10, 11, 18, 19, 24, 42] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 318 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919179 none CC#CCC(NC(=O)C1=NN(C2=CC=C(Cl)C=C2)C(C2=CC=CO2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [196, 196, 196, 114, 54, 54, 12, 54, 12, 12, 12, 12, 19, 19, 17, 17, 19, 19, 1, 1, 1, 1, 1, 1, 12, 114, 154, 154, 196, 196, 196, 196, 196, 114, 54, 19, 19, 19, 19, 1, 1, 1, 12] 201 rigid atoms, others: [39, 40, 41, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42]) total number of confs: 992 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919179 none CC#CCC(NC(=O)C1=NN(C2=CC=C(Cl)C=C2)C(C2=CC=CO2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [150, 150, 150, 67, 28, 28, 5, 28, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 19, 19, 19, 19, 5, 67, 100, 100, 150, 150, 150, 150, 150, 67, 28, 1, 1, 1, 1, 19, 19, 19, 5] 201 rigid atoms, others: [35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42]) total number of confs: 762 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919179 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919179 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919179/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919179 Building REAL300004919180 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919180' /scratch/stefan/7775247/working/building/REAL300004919180 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919180 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919180/0 /scratch/stefan/7775247/working/building/REAL300004919180 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/180 `/scratch/stefan/7775247/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=CC(OC)=CC(OC)=C2N1)C(=O)[O-]) `REAL300004919180.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919180 none CC#CCC(NC(=O)C1=CC2=CC(OC)=CC(OC)=C2N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.pl3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 8, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 38, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 3, 1, 1, 38, 62, 62, 114, 114, 114, 114, 114, 38, 12, 1, 1, 3, 3, 3, 1, 3, 3, 3, 1] 201 rigid atoms, others: [32, 36, 6, 8, 9, 10, 11, 12, 13, 15, 16, 17, 19, 20, 40, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 37, 38, 39]) total number of confs: 546 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919180 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919180 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919180/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919180 Building REAL300004919181 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919181' /scratch/stefan/7775247/working/building/REAL300004919181 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919181 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919181/0 /scratch/stefan/7775247/working/building/REAL300004919181 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/181 `/scratch/stefan/7775247/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(Cl)C2=C(C)C=CC=C2S1)C(=O)[O-]) `REAL300004919181.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919181 none CC#CCC(NC(=O)C1=C(Cl)C2=C(C)C=CC=C2S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 16, 1, 1, 5, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 36, 36, 63, 63, 63, 63, 63, 26, 7, 2, 2, 2, 1, 1, 1] 63 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 283 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919181 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919181 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919181/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919181 Building REAL300004919182 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919182' /scratch/stefan/7775247/working/building/REAL300004919182 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919182 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919182/0 /scratch/stefan/7775247/working/building/REAL300004919182 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/182 `/scratch/stefan/7775247/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCCN1C(=O)OC(C)(C)C)C(=O)[O-]) `REAL300004919182.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919182 none CC#CCC(NC(=O)C1CCCCN1C(=O)OC(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 12, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 11, 13, 13, 13, 12, 17, 17, 25, 25, 25, 25, 25, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13] 45 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 152 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919182 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919182 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919182/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919182 Building REAL300004919183 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919183' /scratch/stefan/7775247/working/building/REAL300004919183 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919183 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919183/0 /scratch/stefan/7775247/working/building/REAL300004919183 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 183) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/183 `/scratch/stefan/7775247/working/3D/183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=CC(Br)=C2)CCCC1)C(=O)[O-]) `REAL300004919183.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919183 none CC#CCC(NC(=O)C1(C2=CC=CC(Br)=C2)CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 33, 11, 11, 1, 11, 1, 1, 9, 9, 4, 9, 9, 9, 1, 1, 1, 1, 33, 55, 55, 96, 96, 96, 96, 96, 33, 11, 9, 9, 8, 9, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 16, 17, 18, 19, 41, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 494 number of broken/clashed sets: 185 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919183 none CC#CCC(NC(=O)C1(C2=CC=CC(Br)=C2)CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 88, 35, 35, 9, 35, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 88, 134, 134, 201, 201, 201, 201, 201, 88, 35, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9] 201 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 1020 number of broken/clashed sets: 185 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919183 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919183 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919183/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919183 Building REAL300004919184 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919184' /scratch/stefan/7775247/working/building/REAL300004919184 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919184 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919184/0 /scratch/stefan/7775247/working/building/REAL300004919184 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/184 `/scratch/stefan/7775247/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CCSC)NC(=O)OC(C)(C)C)C(=O)[O-]) `REAL300004919184.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.0.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.0.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.0.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919184 none CC#CCC(NC(=O)C(CCSC)NC(=O)OC(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 14, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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: [15, 15, 15, 8, 5, 5, 1, 5, 1, 1, 4, 4, 4, 1, 4, 7, 7, 7, 7, 7, 7, 8, 13, 13, 15, 15, 15, 15, 15, 8, 5, 1, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 31 rigid atoms, others: [8, 9, 13, 6, 31] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 120 number of broken/clashed sets: 3 ./output.0.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919184 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919184 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919184/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919184 Building REAL300004919185 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919185' /scratch/stefan/7775247/working/building/REAL300004919185 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919185 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919185/0 /scratch/stefan/7775247/working/building/REAL300004919185 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/185 `/scratch/stefan/7775247/working/3D/185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(NC(=O)OC(C)(C)C)C(C)C)C(=O)[O-]) `REAL300004919185.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.0.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.0.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.0.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919185 none CC#CCC(NC(=O)C(NC(=O)OC(C)(C)C)C(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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: [21, 21, 21, 13, 8, 8, 1, 8, 1, 1, 4, 6, 6, 6, 6, 6, 6, 1, 4, 4, 13, 16, 16, 21, 21, 21, 21, 21, 13, 8, 1, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 5, 5, 5, 5, 5, 5] 31 rigid atoms, others: [8, 9, 30, 6, 17] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 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: 132 number of broken/clashed sets: 0 ./output.0.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919185 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919185 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919185/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919185 Building REAL300004919186 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919186' /scratch/stefan/7775247/working/building/REAL300004919186 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919186 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919186/0 /scratch/stefan/7775247/working/building/REAL300004919186 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/186 `/scratch/stefan/7775247/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CC(C)C)NC(=O)OC(C)(C)C)C(=O)[O-]) `REAL300004919186.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.0.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.0.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.0.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919186 none CC#CCC(NC(=O)C(CC(C)C)NC(=O)OC(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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: [17, 17, 17, 7, 5, 5, 1, 5, 1, 1, 2, 2, 2, 1, 4, 6, 6, 6, 6, 6, 6, 7, 10, 10, 17, 17, 17, 17, 17, 7, 5, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 31 rigid atoms, others: [8, 9, 13, 6, 31] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 99 number of broken/clashed sets: 2 ./output.0.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919186 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919186 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919186/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919186 Building REAL300004919187 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919187' /scratch/stefan/7775247/working/building/REAL300004919187 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919187 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919187/0 /scratch/stefan/7775247/working/building/REAL300004919187 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 187) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/187 `/scratch/stefan/7775247/working/3D/187' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=C(C(C)(C)C)C=C2)CCCCC1)C(=O)[O-]) `REAL300004919187.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919187 none CC#CCC(NC(=O)C1(C2=CC=C(C(C)(C)C)C=C2)CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [77, 77, 77, 20, 5, 5, 1, 5, 1, 1, 7, 7, 1, 1, 9, 9, 9, 7, 7, 1, 1, 1, 1, 1, 20, 34, 34, 77, 77, 77, 77, 77, 20, 5, 7, 7, 10, 9, 9, 10, 9, 9, 10, 9, 9, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 169 rigid atoms, others: [51, 54, 6, 8, 9, 55, 47, 48, 49, 50, 19, 20, 21, 22, 23, 56, 52, 53] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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: 391 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919187 none CC#CCC(NC(=O)C1(C2=CC=C(C(C)(C)C)C=C2)CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [148, 148, 148, 53, 17, 17, 7, 17, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 7, 7, 7, 7, 7, 53, 78, 78, 148, 148, 148, 148, 148, 53, 17, 1, 1, 4, 4, 4, 3, 3, 3, 4, 4, 4, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 169 rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 46, 45, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 717 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919187 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919187 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919187/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919187 Building REAL300004919188 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919188' /scratch/stefan/7775247/working/building/REAL300004919188 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919188 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919188/0 /scratch/stefan/7775247/working/building/REAL300004919188 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/188 `/scratch/stefan/7775247/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=CC=C1C(F)(F)F)C(=O)[O-]) `REAL300004919188.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919188 none CC#CCC(NC(=O)CC1=CC=CC=C1C(F)(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [50, 50, 50, 21, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 21, 30, 30, 50, 50, 50, 50, 50, 21, 7, 2, 2, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919188 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919188 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919188/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919188 Building REAL300004919189 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919189' /scratch/stefan/7775247/working/building/REAL300004919189 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919189 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919189/0 /scratch/stefan/7775247/working/building/REAL300004919189 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/189 `/scratch/stefan/7775247/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=CC(Br)=C1)C(=O)[O-]) `REAL300004919189.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919189 none CC#CCC(NC(=O)CC1=CC=CC(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 68, 19, 19, 8, 19, 1, 1, 1, 1, 1, 1, 1, 1, 68, 114, 114, 201, 201, 201, 201, 201, 68, 19, 8, 8, 1, 1, 1, 1] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 1007 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919189 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919189 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919189/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919189 Building REAL300004919190 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919190' /scratch/stefan/7775247/working/building/REAL300004919190 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919190 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919190/0 /scratch/stefan/7775247/working/building/REAL300004919190 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/190 `/scratch/stefan/7775247/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CSC2=CC=CC=C12)C(=O)[O-]) `REAL300004919190.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919190 none CC#CCC(NC(=O)CC1=CSC2=CC=CC=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 92, 44, 44, 8, 44, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 92, 135, 135, 201, 201, 201, 201, 201, 92, 44, 8, 8, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 989 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919190 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919190 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919190/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919190 Building REAL300004919191 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919191' /scratch/stefan/7775247/working/building/REAL300004919191 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919191 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919191/0 /scratch/stefan/7775247/working/building/REAL300004919191 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/191 `/scratch/stefan/7775247/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)(C)NC(=O)OC(C)(C)C)C(=O)[O-]) `REAL300004919191.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.0.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.0.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.0.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919191 none CC#CCC(NC(=O)C(C)(C)NC(=O)OC(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [21, 21, 21, 12, 6, 6, 1, 6, 1, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 12, 16, 16, 21, 21, 21, 21, 21, 12, 6, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6] 31 rigid atoms, others: [8, 9, 10, 11, 6] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 145 number of broken/clashed sets: 0 ./output.0.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919191 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919191 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919191/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919191 Building REAL300004919192 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919192' /scratch/stefan/7775247/working/building/REAL300004919192 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919192 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919192/0 /scratch/stefan/7775247/working/building/REAL300004919192 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/192 `/scratch/stefan/7775247/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)[C@@H](NC(=O)OC(C)(C)C)C1=CC=CC=C1)C(=O)[O-]) `REAL300004919192.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919192 none CC#CCC(NC(=O)[C@@H](NC(=O)OC(C)(C)C)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 38, 13, 13, 4, 13, 1, 4, 4, 14, 23, 23, 34, 37, 37, 37, 1, 1, 1, 1, 1, 1, 38, 57, 57, 78, 78, 78, 78, 78, 38, 13, 14, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1] 188 rigid atoms, others: [8, 44, 45, 46, 47, 48, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 492 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919192 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919192 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919192/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919192 Building REAL300004919193 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919193' /scratch/stefan/7775247/working/building/REAL300004919193 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919193 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919193/0 /scratch/stefan/7775247/working/building/REAL300004919193 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/193 `/scratch/stefan/7775247/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Cl)=CC=C1Br)C(=O)[O-]) `REAL300004919193.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919193 none CC#CCC(NC(=O)C1=CC(Cl)=CC=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 26, 33, 33, 62, 62, 62, 62, 62, 26, 7, 1, 1, 1] 62 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919193 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919193 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919193/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919193 Building REAL300004919194 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919194' /scratch/stefan/7775247/working/building/REAL300004919194 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919194 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919194/0 /scratch/stefan/7775247/working/building/REAL300004919194 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/194 `/scratch/stefan/7775247/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=CC(I)=C1)C(=O)[O-]) `REAL300004919194.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919194 none CC#CCC(NC(=O)CC1=CC=CC(I)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 18, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 67, 19, 19, 8, 19, 1, 1, 1, 1, 1, 1, 1, 1, 67, 113, 113, 201, 201, 201, 201, 201, 67, 19, 8, 8, 1, 1, 1, 1] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 1007 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919194 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919194 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919194/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919194 Building REAL300004919195 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919195' /scratch/stefan/7775247/working/building/REAL300004919195 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919195 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919195/0 /scratch/stefan/7775247/working/building/REAL300004919195 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/195 `/scratch/stefan/7775247/working/3D/195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=CC(OC)=C(OC)C=C2N1)C(=O)[O-]) `REAL300004919195.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919195 none CC#CCC(NC(=O)C1=CC2=CC(OC)=C(OC)C=C2N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 8, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 131, 45, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 3, 1, 1, 3, 1, 1, 1, 45, 75, 75, 131, 131, 131, 131, 131, 45, 12, 1, 1, 4, 4, 4, 3, 3, 3, 1, 1] 201 rigid atoms, others: [32, 6, 39, 8, 9, 10, 11, 12, 13, 15, 16, 40, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 646 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919195 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919195 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919195/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919195 Building REAL300004919196 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919196' /scratch/stefan/7775247/working/building/REAL300004919196 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919196 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919196/0 /scratch/stefan/7775247/working/building/REAL300004919196 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/196 `/scratch/stefan/7775247/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(I)=CC=C1Cl)C(=O)[O-]) `REAL300004919196.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919196 none CC#CCC(NC(=O)C1=CC(I)=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 18, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 23, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 23, 33, 33, 63, 63, 63, 63, 63, 23, 7, 1, 1, 1] 63 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 280 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919196 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919196 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919196/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919196 Building REAL300004919197 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919197' /scratch/stefan/7775247/working/building/REAL300004919197 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919197 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919197/0 /scratch/stefan/7775247/working/building/REAL300004919197 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 197) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/197 `/scratch/stefan/7775247/working/3D/197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC=C(Br)C=C1)C(=O)[O-]) `REAL300004919197.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919197 none CC#CCC(NC(=O)CCC1=CC=C(Br)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 93, 38, 38, 7, 38, 3, 1, 1, 1, 1, 1, 1, 1, 1, 93, 120, 120, 189, 189, 189, 189, 189, 93, 38, 7, 7, 3, 3, 1, 1, 1, 1] 189 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 881 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919197 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919197 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919197/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919197 Building REAL300004919198 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919198' /scratch/stefan/7775247/working/building/REAL300004919198 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919198 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919198/0 /scratch/stefan/7775247/working/building/REAL300004919198 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/198 `/scratch/stefan/7775247/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)[C@@H](NC(=O)OC(C)(C)C)C(C)(C)C)C(=O)[O-]) `REAL300004919198.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.0.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.0.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.0.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919198 none CC#CCC(NC(=O)[C@@H](NC(=O)OC(C)(C)C)C(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 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: [13, 13, 13, 7, 3, 3, 1, 3, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 1, 2, 2, 2, 7, 9, 9, 13, 13, 13, 13, 13, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2] 31 rigid atoms, others: [8, 9, 10, 18, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 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: 86 number of broken/clashed sets: 0 ./output.0.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919198 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919198 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919198/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919198 Building REAL300004919199 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919199' /scratch/stefan/7775247/working/building/REAL300004919199 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919199 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919199/0 /scratch/stefan/7775247/working/building/REAL300004919199 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 199) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/199 `/scratch/stefan/7775247/working/3D/199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(NC(=O)OC(C)(C)C)CCCC1)C(=O)[O-]) `REAL300004919199.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919199 none CC#CCC(NC(=O)C1(NC(=O)OC(C)(C)C)CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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: [68, 68, 68, 26, 11, 11, 1, 11, 1, 1, 3, 5, 5, 16, 17, 17, 17, 1, 1, 1, 1, 26, 42, 42, 68, 68, 68, 68, 68, 26, 11, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1] 172 rigid atoms, others: [6, 8, 9, 42, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 41] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 362 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919199 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919199 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919199/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919199 Building REAL300004919200 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919200' /scratch/stefan/7775247/working/building/REAL300004919200 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919200 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919200/0 /scratch/stefan/7775247/working/building/REAL300004919200 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/200 `/scratch/stefan/7775247/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC(NC(=O)OC(C)(C)C)C1=CC=CC=C1)C(=O)[O-]) `REAL300004919200.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919200 none CC#CCC(NC(=O)CC(NC(=O)OC(C)(C)C)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 18, 10, 10, 5, 10, 3, 1, 3, 5, 8, 8, 19, 21, 21, 21, 1, 1, 1, 1, 1, 1, 18, 23, 23, 38, 38, 38, 38, 38, 18, 10, 5, 5, 3, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1] 70 rigid atoms, others: [51, 9, 50, 47, 48, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919200 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919200 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919200/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919200 Building REAL300004919201 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919201' /scratch/stefan/7775247/working/building/REAL300004919201 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919201 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919201/0 /scratch/stefan/7775247/working/building/REAL300004919201 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/201 `/scratch/stefan/7775247/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCN1S(=O)(=O)CCCC)C(=O)[O-]) `REAL300004919201.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919201 none CC#CCC(NC(=O)C1CCCN1S(=O)(=O)CCCC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 8, 14, 11, 11, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 24, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 18, 31, 24, 36, 36, 70, 70, 70, 70, 70, 24, 8, 1, 1, 1, 1, 1, 1, 1, 12, 12, 18, 18, 32, 32, 31, 32, 32] 201 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 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]) total number of confs: 467 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919201 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919201 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919201/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919201 Building REAL300004919202 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919202' /scratch/stefan/7775247/working/building/REAL300004919202 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919202 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919202/0 /scratch/stefan/7775247/working/building/REAL300004919202 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/202 `/scratch/stefan/7775247/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(SC(C)C)C=C1)C(=O)[O-]) `REAL300004919202.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919202 none CC#CCC(NC(=O)C1=CC=C(SC(C)C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 14, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 13, 30, 30, 1, 1, 10, 17, 17, 41, 41, 41, 41, 41, 10, 4, 1, 1, 30, 30, 30, 30, 30, 30, 30, 1, 1] 201 rigid atoms, others: [37, 6, 8, 9, 10, 11, 12, 16, 17, 38, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 269 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919202 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919202 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919202/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919202 Building REAL300004919203 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919203' /scratch/stefan/7775247/working/building/REAL300004919203 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919203 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919203/0 /scratch/stefan/7775247/working/building/REAL300004919203 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/203 `/scratch/stefan/7775247/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1(CS(C)(=O)=O)CC1)C(=O)[O-]) `REAL300004919203.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919203 none CC#CCC(NC(=O)CC1(CS(C)(=O)=O)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 5, 5, 14, 5, 11, 11, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [129, 129, 129, 58, 25, 25, 6, 25, 1, 1, 1, 5, 11, 11, 11, 1, 1, 58, 92, 92, 129, 129, 129, 129, 129, 58, 25, 6, 6, 5, 5, 11, 11, 11, 1, 1, 1, 1] 168 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 701 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919203 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919203 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919203/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919203 Building REAL300004919204 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919204' /scratch/stefan/7775247/working/building/REAL300004919204 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919204 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919204/0 /scratch/stefan/7775247/working/building/REAL300004919204 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/204 `/scratch/stefan/7775247/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1OC1=CC=CC=C1OCC)C(=O)[O-]) `REAL300004919204.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919204 none CC#CCC(NC(=O)C1=CC=CC=C1OC1=CC=CC=C1OCC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 11, 13, 13, 13, 31, 52, 19, 31, 31, 50, 50, 50, 50, 50, 19, 11, 1, 1, 1, 1, 13, 13, 13, 13, 52, 52, 52, 52, 52] 201 rigid atoms, others: [34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 7, 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]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919204 none CC#CCC(NC(=O)C1=CC=CC=C1OC1=CC=CC=C1OCC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 158, 78, 60, 60, 13, 60, 13, 13, 12, 13, 13, 8, 1, 1, 1, 1, 1, 1, 1, 1, 9, 28, 78, 110, 110, 158, 158, 158, 158, 158, 78, 60, 13, 13, 13, 13, 1, 1, 1, 1, 28, 28, 29, 29, 29] 201 rigid atoms, others: [38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 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: 849 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919204 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919204 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919204/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919204 Building REAL300004919205 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919205' /scratch/stefan/7775247/working/building/REAL300004919205 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919205 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919205/0 /scratch/stefan/7775247/working/building/REAL300004919205 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/205 `/scratch/stefan/7775247/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C(=O)C2=CNC=C2)C=C1)C(=O)[O-]) `REAL300004919205.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919205 none CC#CCC(NC(=O)C1=CC=C(C(=O)C2=CNC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 13, 13, 39, 39, 39, 39, 1, 1, 8, 12, 12, 23, 23, 23, 23, 23, 8, 3, 1, 1, 39, 39, 39, 39, 1, 1] 201 rigid atoms, others: [32, 37, 6, 8, 9, 10, 11, 12, 19, 20, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36]) total number of confs: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919205 none CC#CCC(NC(=O)C1=CC=C(C(=O)C2=CNC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 68, 68, 39, 68, 21, 39, 39, 11, 1, 11, 1, 1, 1, 1, 1, 39, 39, 119, 149, 149, 201, 201, 201, 201, 201, 119, 68, 39, 39, 1, 1, 1, 1, 39, 39] 201 rigid atoms, others: [33, 34, 35, 36, 12, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 1032 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919205 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919205 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919205/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919205 Building REAL300004919206 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919206' /scratch/stefan/7775247/working/building/REAL300004919206 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919206 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919206/0 /scratch/stefan/7775247/working/building/REAL300004919206 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/206 `/scratch/stefan/7775247/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(SC2=CC=C(C)C=C2)CCCC1)C(=O)[O-]) `REAL300004919206.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919206 none CC#CCC(NC(=O)C1(SC2=CC=C(C)C=C2)CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 14, 1, 1, 1, 1, 5, 1, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 14, 7, 7, 1, 7, 1, 1, 8, 10, 10, 9, 9, 10, 10, 1, 1, 1, 1, 14, 14, 14, 27, 27, 27, 27, 27, 14, 7, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1] 36 rigid atoms, others: [38, 6, 39, 8, 9, 42, 43, 44, 45, 17, 18, 19, 20, 41, 40] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 138 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: REAL300004919206 none CC#CCC(NC(=O)C1(SC2=CC=C(C)C=C2)CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 14, 1, 1, 1, 1, 5, 1, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 26, 18, 18, 10, 18, 4, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 26, 26, 26, 36, 36, 36, 36, 36, 26, 18, 1, 1, 2, 2, 2, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10] 36 rigid atoms, others: [32, 36, 37, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 165 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919206 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919206 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919206/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919206 Building REAL300004919207 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919207' /scratch/stefan/7775247/working/building/REAL300004919207 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919207 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919207/0 /scratch/stefan/7775247/working/building/REAL300004919207 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/207 `/scratch/stefan/7775247/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(SC)=C(Cl)C=C1Cl)C(=O)[O-]) `REAL300004919207.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919207 none CC#CCC(NC(=O)C1=CC(SC)=C(Cl)C=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 14, 5, 1, 16, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [91, 91, 91, 29, 7, 7, 1, 7, 1, 1, 1, 1, 9, 1, 1, 1, 1, 1, 29, 46, 46, 91, 91, 91, 91, 91, 29, 7, 1, 10, 10, 10, 1] 180 rigid atoms, others: [32, 6, 8, 9, 10, 11, 13, 14, 15, 16, 17, 28] set([0, 1, 2, 3, 4, 5, 7, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 419 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919207 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919207 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919207/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919207 Building REAL300004919208 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919208' /scratch/stefan/7775247/working/building/REAL300004919208 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919208 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919208/0 /scratch/stefan/7775247/working/building/REAL300004919208 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/208 `/scratch/stefan/7775247/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC=C(OC)C(C)=C1)C(=O)[O-]) `REAL300004919208.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919208 none CC#CCC(NC(=O)COC1=CC=C(OC)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 189, 134, 79, 79, 19, 79, 6, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 134, 153, 153, 189, 189, 189, 189, 189, 134, 79, 19, 19, 1, 1, 4, 4, 4, 2, 2, 2, 1] 201 rigid atoms, others: [32, 39, 9, 10, 11, 12, 13, 14, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 887 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919208 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919208 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919208/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919208 Building REAL300004919209 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919209' /scratch/stefan/7775247/working/building/REAL300004919209 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919209 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919209/0 /scratch/stefan/7775247/working/building/REAL300004919209 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/209 `/scratch/stefan/7775247/working/3D/209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(OCC2=CC=CC=C2)CCOCC1)C(=O)[O-]) `REAL300004919209.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919209 none CC#CCC(NC(=O)C1(OCC2=CC=CC=C2)CCOCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 16, 5, 5, 1, 5, 1, 1, 7, 13, 25, 25, 13, 25, 25, 1, 1, 1, 1, 1, 16, 18, 18, 37, 37, 37, 37, 37, 16, 5, 13, 13, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1] 60 rigid atoms, others: [6, 39, 8, 9, 41, 43, 44, 45, 46, 17, 18, 19, 20, 21, 40, 42] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 263 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: REAL300004919209 none CC#CCC(NC(=O)C1(OCC2=CC=CC=C2)CCOCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 50, 33, 33, 25, 33, 10, 3, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 50, 52, 52, 60, 60, 60, 60, 60, 50, 33, 3, 3, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25] 60 rigid atoms, others: [34, 35, 36, 37, 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, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 255 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919209 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919209 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919209/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919209 Building REAL300004919210 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919210' /scratch/stefan/7775247/working/building/REAL300004919210 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919210 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919210/0 /scratch/stefan/7775247/working/building/REAL300004919210 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/210 `/scratch/stefan/7775247/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C12CCC(CC1Br)C2)C(=O)[O-]) `REAL300004919210.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919210 none CC#CCC(NC(=O)C12CCC(CC1Br)C2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'Br', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 17, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 29, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 29, 44, 44, 82, 82, 82, 82, 82, 29, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 82 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 375 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919210 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919210 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919210/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919210 Building REAL300004919211 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919211' /scratch/stefan/7775247/working/building/REAL300004919211 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919211 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919211/0 /scratch/stefan/7775247/working/building/REAL300004919211 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 211) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/211 `/scratch/stefan/7775247/working/3D/211' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC=CC(OCC(C)C)=C1)C(=O)[O-]) `REAL300004919211.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919211 none CC#CCC(NC(=O)COC1=CC=CC(OCC(C)C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 32, 32, 32, 15, 32, 7, 1, 1, 1, 1, 1, 1, 1, 6, 8, 15, 15, 1, 32, 51, 51, 59, 59, 59, 59, 59, 32, 32, 15, 15, 1, 1, 1, 8, 8, 15, 15, 15, 15, 15, 15, 15, 1] 201 rigid atoms, others: [33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 20, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 390 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919211 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919211 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919211/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919211 Building REAL300004919212 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919212' /scratch/stefan/7775247/working/building/REAL300004919212 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919212 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919212/0 /scratch/stefan/7775247/working/building/REAL300004919212 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/212 `/scratch/stefan/7775247/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=COC(S(=O)(=O)N(C)C)=C1)C(=O)[O-]) `REAL300004919212.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919212 none CC#CCC(NC(=O)C1=COC(S(=O)(=O)N(C)C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 12, 1, 14, 11, 11, 8, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 8, 8, 8, 16, 16, 1, 17, 27, 27, 50, 50, 50, 50, 50, 17, 5, 1, 17, 17, 17, 17, 17, 17, 1] 201 rigid atoms, others: [36, 6, 8, 9, 10, 11, 12, 18, 29] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 300 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919212 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919212 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919212/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919212 Building REAL300004919213 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919213' /scratch/stefan/7775247/working/building/REAL300004919213 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919213 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919213/0 /scratch/stefan/7775247/working/building/REAL300004919213 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 213) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/213 `/scratch/stefan/7775247/working/3D/213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(OC)CCN(C(=O)OC(C)(C)C)CC1)C(=O)[O-]) `REAL300004919213.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919213 none CC#CCC(NC(=O)C1(OC)CCN(C(=O)OC(C)(C)C)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 28, 11, 11, 1, 11, 1, 1, 5, 1, 1, 1, 1, 6, 6, 15, 17, 17, 17, 1, 1, 28, 42, 42, 62, 62, 62, 62, 62, 28, 11, 5, 5, 5, 1, 1, 1, 1, 18, 18, 18, 17, 17, 17, 18, 18, 18, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 6, 39, 8, 9, 11, 12, 13, 14, 49, 50, 51, 52, 21, 22, 38] set([0, 1, 2, 3, 4, 5, 7, 10, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 357 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919213 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919213 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919213/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919213 Building REAL300004919214 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919214' /scratch/stefan/7775247/working/building/REAL300004919214 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919214 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919214/0 /scratch/stefan/7775247/working/building/REAL300004919214 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/214 `/scratch/stefan/7775247/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=CC=CC=C2C=C1NC(=O)OC(C)(C)C)C(=O)[O-]) `REAL300004919214.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919214 none CC#CCC(NC(=O)C1=CC2=CC=CC=C2C=C1NC(=O)OC(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 41, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919214 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919214 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919214/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919214 Building REAL300004919215 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919215' /scratch/stefan/7775247/working/building/REAL300004919215 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919215 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919215/0 /scratch/stefan/7775247/working/building/REAL300004919215 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 215) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/215 `/scratch/stefan/7775247/working/3D/215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=CC(Br)=C2)CCC1)C(=O)[O-]) `REAL300004919215.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919215 none CC#CCC(NC(=O)C1(C2=CC=CC(Br)=C2)CCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 35, 11, 11, 1, 11, 1, 1, 9, 9, 4, 9, 9, 9, 1, 1, 1, 35, 55, 55, 93, 93, 93, 93, 93, 35, 11, 9, 9, 7, 9, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 16, 17, 18, 38] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 462 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919215 none CC#CCC(NC(=O)C1(C2=CC=CC(Br)=C2)CCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 1, 1, 1, 1, 1, 17, 1, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 100, 47, 47, 9, 47, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 100, 136, 136, 201, 201, 201, 201, 201, 100, 47, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9] 201 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38]) total number of confs: 951 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919215 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919215 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919215/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919215 Building REAL300004919216 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919216' /scratch/stefan/7775247/working/building/REAL300004919216 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919216 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919216/0 /scratch/stefan/7775247/working/building/REAL300004919216 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/216 `/scratch/stefan/7775247/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(N2C=CC(C)=N2)=C1)C(=O)[O-]) `REAL300004919216.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919216 none CC#CCC(NC(=O)C1=CC=CC(N2C=CC(C)=N2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 1, 1, 5, 8, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 29, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 6, 6, 6, 7, 7, 1, 29, 48, 48, 96, 96, 96, 96, 96, 29, 7, 1, 1, 1, 7, 7, 7, 7, 7, 1] 162 rigid atoms, others: [32, 38, 6, 8, 9, 10, 11, 12, 13, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37]) total number of confs: 447 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919216 none CC#CCC(NC(=O)C1=CC=CC(N2C=CC(C)=N2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 1, 1, 5, 8, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [162, 162, 162, 74, 25, 25, 7, 25, 7, 6, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 74, 99, 99, 162, 162, 162, 162, 162, 74, 25, 6, 7, 7, 1, 1, 2, 2, 2, 7] 162 rigid atoms, others: [33, 34, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38]) total number of confs: 744 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919216 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919216 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919216/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919216 Building REAL300004919217 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919217' /scratch/stefan/7775247/working/building/REAL300004919217 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919217 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919217/0 /scratch/stefan/7775247/working/building/REAL300004919217 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 217) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/217 `/scratch/stefan/7775247/working/3D/217' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C(C)C)N1N=NC(C2=CC=CC=C2)=N1)C(=O)[O-]) `REAL300004919217.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919217 none CC#CCC(NC(=O)C(C(C)C)N1N=NC(C2=CC=CC=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [31, 31, 31, 27, 20, 20, 6, 20, 1, 6, 8, 8, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 27, 27, 27, 31, 31, 31, 31, 31, 27, 20, 6, 8, 8, 8, 8, 8, 8, 8, 4, 4, 3, 4, 4] 31 rigid atoms, others: [8, 12, 13, 14, 15, 16, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919217 none CC#CCC(NC(=O)C(C(C)C)N1N=NC(C2=CC=CC=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [31, 31, 31, 29, 22, 22, 11, 22, 4, 11, 12, 12, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 29, 29, 29, 31, 31, 31, 31, 31, 29, 22, 11, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1] 31 rigid atoms, others: [41, 42, 43, 44, 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919217 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919217 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919217/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919217 Building REAL300004919218 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919218' /scratch/stefan/7775247/working/building/REAL300004919218 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919218 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919218/0 /scratch/stefan/7775247/working/building/REAL300004919218 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/218 `/scratch/stefan/7775247/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)[C@H]1CCCCN1C(=O)OC(C)(C)C)C(=O)[O-]) `REAL300004919218.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919218 none CC#CCC(NC(=O)[C@H]1CCCCN1C(=O)OC(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 7, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [38, 38, 38, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 16, 16, 16, 14, 22, 22, 38, 38, 38, 38, 38, 14, 5, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16] 71 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 15, 38] set([0, 1, 2, 3, 4, 5, 7, 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]) total number of confs: 215 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919218 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919218 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919218/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919218 Building REAL300004919219 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919219' /scratch/stefan/7775247/working/building/REAL300004919219 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919219 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919219/0 /scratch/stefan/7775247/working/building/REAL300004919219 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 219) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/219 `/scratch/stefan/7775247/working/3D/219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)[C@@H]1CCCN1C(=O)OC(C)(C)C)C(=O)[O-]) `REAL300004919219.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919219 none CC#CCC(NC(=O)[C@@H]1CCCN1C(=O)OC(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 29, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 14, 14, 14, 29, 45, 45, 78, 78, 78, 78, 78, 29, 10, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15] 201 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 416 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919219 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919219 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919219/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919219 Building REAL300004919220 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919220' /scratch/stefan/7775247/working/building/REAL300004919220 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919220 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919220/0 /scratch/stefan/7775247/working/building/REAL300004919220 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/220 `/scratch/stefan/7775247/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)[C@@H]1CCCCN1C(=O)OC(C)(C)C)C(=O)[O-]) `REAL300004919220.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919220 none CC#CCC(NC(=O)[C@@H]1CCCCN1C(=O)OC(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 7, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 12, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 11, 12, 12, 12, 12, 17, 17, 25, 25, 25, 25, 25, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12] 44 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 15, 38] set([0, 1, 2, 3, 4, 5, 7, 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]) total number of confs: 146 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919220 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919220 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919220/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919220 Building REAL300004919221 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919221' /scratch/stefan/7775247/working/building/REAL300004919221 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919221 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919221/0 /scratch/stefan/7775247/working/building/REAL300004919221 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/221 `/scratch/stefan/7775247/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)[C@H](CCSC)NC(=O)OC(C)(C)C)C(=O)[O-]) `REAL300004919221.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.0.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.0.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.0.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919221 none CC#CCC(NC(=O)[C@H](CCSC)NC(=O)OC(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 7, 5, 5, 14, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [14, 14, 14, 8, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 1, 4, 7, 7, 7, 7, 7, 7, 8, 13, 13, 14, 14, 14, 14, 14, 8, 5, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 31 rigid atoms, others: [8, 9, 10, 14, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 114 number of broken/clashed sets: 3 ./output.0.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919221 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919221 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919221/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919221 Building REAL300004919222 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919222' /scratch/stefan/7775247/working/building/REAL300004919222 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919222 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919222/0 /scratch/stefan/7775247/working/building/REAL300004919222 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/222 `/scratch/stefan/7775247/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=CC=C2C)CCOCC1)C(=O)[O-]) `REAL300004919222.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919222 none CC#CCC(NC(=O)C1(C2=CC=CC=C2C)CCOCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 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: [37, 37, 37, 15, 5, 5, 1, 5, 1, 1, 5, 5, 1, 5, 5, 5, 1, 1, 1, 1, 1, 15, 22, 22, 37, 37, 37, 37, 37, 15, 5, 5, 5, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1] 41 rigid atoms, others: [38, 6, 39, 8, 9, 42, 43, 45, 44, 16, 17, 18, 19, 20, 41, 40] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 182 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919222 none CC#CCC(NC(=O)C1(C2=CC=CC=C2C)CCOCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 18, 7, 7, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 18, 25, 25, 41, 41, 41, 41, 41, 18, 7, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5] 41 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 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]) total number of confs: 197 number of broken/clashed sets: 41 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919222 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919222 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919222/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919222 Building REAL300004919223 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919223' /scratch/stefan/7775247/working/building/REAL300004919223 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919223 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919223/0 /scratch/stefan/7775247/working/building/REAL300004919223 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 223) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/223 `/scratch/stefan/7775247/working/3D/223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C2=CC=CC=C2)C2=CC=C(OC)C=C2O1)C(=O)[O-]) `REAL300004919223.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919223 none CC#CCC(NC(=O)C1=C(C2=CC=CC=C2)C2=CC=C(OC)C=C2O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 133, 47, 13, 13, 1, 13, 1, 1, 1, 5, 5, 1, 5, 5, 1, 1, 1, 1, 1, 2, 1, 1, 1, 47, 76, 76, 133, 133, 133, 133, 133, 47, 13, 5, 5, 1, 5, 5, 1, 1, 3, 3, 3, 1] 201 rigid atoms, others: [6, 8, 9, 10, 45, 16, 17, 18, 19, 40, 41, 22, 23, 24, 20] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 642 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919223 none CC#CCC(NC(=O)C1=C(C2=CC=CC=C2)C2=CC=C(OC)C=C2O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [179, 179, 179, 84, 31, 31, 5, 31, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 5, 5, 5, 84, 120, 120, 179, 179, 179, 179, 179, 84, 31, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 5] 201 rigid atoms, others: [35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45]) total number of confs: 862 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919223 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919223 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919223/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919223 Building REAL300004919224 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919224' /scratch/stefan/7775247/working/building/REAL300004919224 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919224 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919224/0 /scratch/stefan/7775247/working/building/REAL300004919224 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/224 `/scratch/stefan/7775247/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1CCCN1C(=O)OC(C)(C)C)C(=O)[O-]) `REAL300004919224.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919224 none CC#CCC(NC(=O)CC1CCCN1C(=O)OC(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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, 4, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 4, 4, 4, 5, 5, 5, 5, 5, 4, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3] 5 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919224 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919224 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919224/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919224 Building REAL300004919225 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919225' /scratch/stefan/7775247/working/building/REAL300004919225 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919225 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919225/0 /scratch/stefan/7775247/working/building/REAL300004919225 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/225 `/scratch/stefan/7775247/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1OC1=CC=C(Cl)C=C1Cl)C(=O)[O-]) `REAL300004919225.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919225 none CC#CCC(NC(=O)C1=CC=CC=C1OC1=CC=C(Cl)C=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 35, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 6, 10, 10, 6, 9, 10, 10, 10, 35, 51, 51, 87, 87, 87, 87, 87, 35, 12, 1, 1, 1, 1, 10, 10, 10] 201 rigid atoms, others: [33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39]) total number of confs: 436 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: REAL300004919225 none CC#CCC(NC(=O)C1=CC=CC=C1OC1=CC=C(Cl)C=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 104, 58, 58, 10, 58, 10, 10, 10, 10, 10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 104, 140, 140, 201, 201, 201, 201, 201, 104, 58, 10, 10, 10, 10, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 962 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919225 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919225 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919225/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919225 Building REAL300004919226 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919226' /scratch/stefan/7775247/working/building/REAL300004919226 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919226 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919226/0 /scratch/stefan/7775247/working/building/REAL300004919226 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/226 `/scratch/stefan/7775247/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN=NN1C1=CC=CC=C1Cl)C(=O)[O-]) `REAL300004919226.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919226 none CC#CCC(NC(=O)C1=CN=NN1C1=CC=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 44, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 9, 9, 1, 9, 9, 9, 44, 69, 69, 108, 108, 108, 108, 108, 44, 13, 1, 9, 9, 2, 9] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 30] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919226 none CC#CCC(NC(=O)C1=CN=NN1C1=CC=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 108, 48, 48, 9, 48, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 108, 141, 141, 201, 201, 201, 201, 201, 108, 48, 9, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 917 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919226 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919226 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919226/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919226 Building REAL300004919227 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919227' /scratch/stefan/7775247/working/building/REAL300004919227 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919227 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919227/0 /scratch/stefan/7775247/working/building/REAL300004919227 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/227 `/scratch/stefan/7775247/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1C2=CC=CC=C2CCN1C(=O)OC(C)(C)C)C(=O)[O-]) `REAL300004919227.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919227 none CC#CCC(NC(=O)C1C2=CC=CC=C2CCN1C(=O)OC(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 29, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 18, 18, 18, 29, 45, 45, 71, 71, 71, 71, 71, 29, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19] 201 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 41, 43, 40, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 410 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919227 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919227 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919227/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919227 Building REAL300004919228 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919228' /scratch/stefan/7775247/working/building/REAL300004919228 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919228 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919228/0 /scratch/stefan/7775247/working/building/REAL300004919228 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/228 `/scratch/stefan/7775247/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CC1=CC=CC=C1)NC(=O)OC(C)(C)C)C(=O)[O-]) `REAL300004919228.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919228 none CC#CCC(NC(=O)C(CC1=CC=CC=C1)NC(=O)OC(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 98, 45, 24, 24, 6, 24, 2, 1, 1, 1, 1, 1, 1, 1, 6, 19, 29, 29, 38, 40, 40, 40, 45, 63, 63, 98, 98, 98, 98, 98, 45, 24, 6, 2, 2, 1, 1, 1, 1, 1, 19, 40, 40, 40, 40, 40, 40, 40, 40, 40] 201 rigid atoms, others: [37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 41] 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 575 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919228 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919228 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919228/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919228 Building REAL300004919229 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919229' /scratch/stefan/7775247/working/building/REAL300004919229 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919229 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919229/0 /scratch/stefan/7775247/working/building/REAL300004919229 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/229 `/scratch/stefan/7775247/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC=C(Br)C=C1F)C(=O)[O-]) `REAL300004919229.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919229 none CC#CCC(NC(=O)CCC1=CC=C(Br)C=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 17, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 106, 54, 54, 15, 54, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 106, 141, 141, 201, 201, 201, 201, 201, 106, 54, 15, 15, 7, 7, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 974 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919229 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919229 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919229/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919229 Building REAL300004919230 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919230' /scratch/stefan/7775247/working/building/REAL300004919230 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919230 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919230/0 /scratch/stefan/7775247/working/building/REAL300004919230 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/230 `/scratch/stefan/7775247/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCN(S(=O)(=O)C2=CN(C)C(C)=N2)CC1)C(=O)[O-]) `REAL300004919230.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919230 none CC#CCC(NC(=O)C1CCN(S(=O)(=O)C2=CN(C)C(C)=N2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 8, 14, 11, 11, 1, 1, 8, 5, 1, 5, 8, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 27, 11, 11, 1, 11, 1, 1, 1, 1, 1, 3, 3, 3, 18, 18, 18, 18, 18, 18, 1, 1, 27, 42, 42, 55, 55, 55, 55, 55, 27, 11, 1, 1, 1, 1, 1, 18, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 46, 47, 48, 49, 22, 23, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 311 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919230 none CC#CCC(NC(=O)C1CCN(S(=O)(=O)C2=CN(C)C(C)=N2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 8, 14, 11, 11, 1, 1, 8, 5, 1, 5, 8, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 135, 81, 81, 18, 81, 18, 18, 18, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 18, 18, 135, 161, 161, 201, 201, 201, 201, 201, 135, 81, 18, 18, 18, 18, 18, 1, 2, 2, 2, 2, 2, 2, 18, 18, 18, 18] 201 rigid atoms, others: [39, 12, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 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: 947 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919230 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919230 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919230/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919230 Building REAL300004919231 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919231' /scratch/stefan/7775247/working/building/REAL300004919231 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919231 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919231/0 /scratch/stefan/7775247/working/building/REAL300004919231 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 231) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/231 `/scratch/stefan/7775247/working/3D/231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)C2CCCC2)C=C1)C(=O)[O-]) `REAL300004919231.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919231 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)C2CCCC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 2, 2, 2, 16, 16, 16, 16, 1, 1, 16, 25, 25, 56, 56, 56, 56, 56, 16, 4, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1] 201 rigid atoms, others: [32, 33, 43, 6, 8, 9, 10, 11, 12, 44, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919231 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)C2CCCC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 102, 33, 33, 9, 33, 9, 16, 16, 9, 1, 9, 9, 1, 1, 1, 1, 1, 16, 16, 102, 131, 131, 201, 201, 201, 201, 201, 102, 33, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 991 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919231 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919231 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919231/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919231 Building REAL300004919232 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919232' /scratch/stefan/7775247/working/building/REAL300004919232 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919232 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919232/0 /scratch/stefan/7775247/working/building/REAL300004919232 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/232 `/scratch/stefan/7775247/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=C(C)C1=CC=C(C(F)(F)F)C=C1)C(=O)[O-]) `REAL300004919232.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919232 none CC#CCC(NC(=O)C=C(C)C1=CC=C(C(F)(F)F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [138, 138, 138, 88, 38, 38, 6, 38, 6, 1, 6, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 88, 112, 112, 138, 138, 138, 138, 138, 88, 38, 6, 6, 6, 6, 1, 1, 1, 1] 138 rigid atoms, others: [35, 36, 37, 38, 9, 11, 12, 13, 14, 15, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 669 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919232 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919232 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919232/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919232 Building REAL300004919233 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919233' /scratch/stefan/7775247/working/building/REAL300004919233 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919233 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919233/0 /scratch/stefan/7775247/working/building/REAL300004919233 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/233 `/scratch/stefan/7775247/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(N2CCCS2(=O)=O)C=C1Cl)C(=O)[O-]) `REAL300004919233.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919233 none CC#CCC(NC(=O)C1=CC=C(N2CCCS2(=O)=O)C=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 5, 14, 11, 11, 1, 1, 16, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 16, 7, 7, 1, 7, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 1, 1, 1, 16, 26, 26, 43, 43, 43, 43, 43, 16, 7, 1, 1, 13, 13, 13, 13, 13, 13, 1] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 40, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919233 none CC#CCC(NC(=O)C1=CC=C(N2CCCS2(=O)=O)C=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 5, 14, 11, 11, 1, 1, 16, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 109, 51, 51, 12, 51, 11, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 109, 135, 135, 201, 201, 201, 201, 201, 109, 51, 13, 13, 1, 1, 1, 1, 1, 1, 13] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40]) total number of confs: 925 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919233 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919233 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919233/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919233 Building REAL300004919234 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919234' /scratch/stefan/7775247/working/building/REAL300004919234 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919234 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919234/0 /scratch/stefan/7775247/working/building/REAL300004919234 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/234 `/scratch/stefan/7775247/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=CC=C2C)CCCCC1)C(=O)[O-]) `REAL300004919234.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919234 none CC#CCC(NC(=O)C1(C2=CC=CC=C2C)CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 14, 5, 5, 1, 5, 1, 1, 5, 5, 1, 5, 5, 5, 1, 1, 1, 1, 1, 14, 20, 20, 35, 35, 35, 35, 35, 14, 5, 5, 5, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 40 rigid atoms, others: [38, 6, 39, 8, 9, 42, 43, 45, 46, 44, 16, 17, 18, 19, 20, 41, 40, 47] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 166 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919234 none CC#CCC(NC(=O)C1(C2=CC=CC=C2C)CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 18, 7, 7, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 18, 23, 23, 40, 40, 40, 40, 40, 18, 7, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 40 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 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]) total number of confs: 180 number of broken/clashed sets: 34 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919234 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919234 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919234/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919234 Building REAL300004919235 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919235' /scratch/stefan/7775247/working/building/REAL300004919235 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919235 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919235/0 /scratch/stefan/7775247/working/building/REAL300004919235 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/235 `/scratch/stefan/7775247/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(Br)C(S(C)(=O)=O)=C1)C(=O)[O-]) `REAL300004919235.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919235 none CC#CCC(NC(=O)C1=CC=C(Br)C(S(C)(=O)=O)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 17, 1, 14, 5, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 30, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 30, 46, 46, 95, 95, 95, 95, 95, 30, 7, 1, 1, 4, 4, 4, 1] 161 rigid atoms, others: [34, 6, 8, 9, 10, 11, 12, 13, 14, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33]) total number of confs: 430 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919235 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919235 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919235/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919235 Building REAL300004919236 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919236' /scratch/stefan/7775247/working/building/REAL300004919236 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919236 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919236/0 /scratch/stefan/7775247/working/building/REAL300004919236 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/236 `/scratch/stefan/7775247/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(CN2C=C(Cl)C=N2)O1)C(=O)[O-]) `REAL300004919236.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919236 none CC#CCC(NC(=O)C1=CC=C(CN2C=C(Cl)C=N2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 1, 16, 1, 8, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 6, 6, 1, 6, 1, 1, 1, 1, 1, 9, 25, 25, 25, 25, 25, 1, 19, 28, 28, 45, 45, 45, 45, 45, 19, 6, 1, 1, 9, 9, 25, 25] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) 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: REAL300004919236 none CC#CCC(NC(=O)C1=CC=C(CN2C=C(Cl)C=N2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 1, 16, 1, 8, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 115, 58, 58, 25, 58, 25, 25, 25, 7, 1, 1, 1, 1, 1, 1, 1, 25, 115, 147, 147, 201, 201, 201, 201, 201, 115, 58, 25, 25, 7, 7, 1, 1] 201 rigid atoms, others: [34, 35, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 951 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919236 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919236 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919236/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919236 Building REAL300004919237 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919237' /scratch/stefan/7775247/working/building/REAL300004919237 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919237 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919237/0 /scratch/stefan/7775247/working/building/REAL300004919237 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/237 `/scratch/stefan/7775247/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C)=CC=C1I)C(=O)[O-]) `REAL300004919237.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919237 none CC#CCC(NC(=O)C1=CC(C)=CC=C1I)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 5, 1, 1, 1, 18, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 24, 36, 36, 53, 53, 53, 53, 53, 24, 7, 1, 2, 2, 2, 1, 1] 53 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 26, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29]) total number of confs: 267 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919237 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919237 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919237/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919237 Building REAL300004919238 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919238' /scratch/stefan/7775247/working/building/REAL300004919238 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919238 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919238/0 /scratch/stefan/7775247/working/building/REAL300004919238 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/238 `/scratch/stefan/7775247/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CSCN1C(=O)OC(C)(C)C)C(=O)[O-]) `REAL300004919238.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919238 none CC#CCC(NC(=O)C1CSCN1C(=O)OC(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 14, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 2, 2, 7, 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: [71, 71, 71, 23, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 15, 18, 18, 18, 23, 38, 38, 71, 71, 71, 71, 71, 23, 8, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19] 174 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 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]) total number of confs: 389 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919238 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919238 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919238/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919238 Building REAL300004919239 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919239' /scratch/stefan/7775247/working/building/REAL300004919239 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919239 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919239/0 /scratch/stefan/7775247/working/building/REAL300004919239 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/239 `/scratch/stefan/7775247/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)C1=C(Cl)C=CC=C1Cl)C(=O)[O-]) `REAL300004919239.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919239 none CC#CCC(NC(=O)C(C)C1=C(Cl)C=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 16, 1, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 18, 6, 6, 2, 6, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 18, 28, 28, 48, 48, 48, 48, 48, 18, 6, 2, 2, 2, 2, 1, 1, 1] 48 rigid atoms, others: [32, 33, 34, 8, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919239 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919239 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919239/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919239 Building REAL300004919240 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919240' /scratch/stefan/7775247/working/building/REAL300004919240 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919240 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919240/0 /scratch/stefan/7775247/working/building/REAL300004919240 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/240 `/scratch/stefan/7775247/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C)=C(C2=CC=C(F)C=C2)S1)C(=O)[O-]) `REAL300004919240.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919240 none CC#CCC(NC(=O)C1=CC(C)=C(C2=CC=C(F)C=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 5, 1, 1, 1, 1, 1, 15, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 43, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 4, 4, 2, 3, 4, 4, 1, 43, 67, 67, 105, 105, 105, 105, 105, 43, 13, 1, 2, 2, 2, 4, 4, 4, 4] 110 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 526 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919240 none CC#CCC(NC(=O)C1=CC(C)=C(C2=CC=C(F)C=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 5, 1, 1, 1, 1, 1, 15, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 110, 73, 35, 35, 4, 35, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 73, 87, 87, 110, 110, 110, 110, 110, 73, 35, 4, 4, 4, 4, 1, 1, 1, 1] 110 rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 495 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919240 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919240 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919240/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919240 Building REAL300004919241 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919241' /scratch/stefan/7775247/working/building/REAL300004919241 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919241 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919241/0 /scratch/stefan/7775247/working/building/REAL300004919241 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/241 `/scratch/stefan/7775247/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(NC(=O)OC(C)(C)C)C(C)(C)C)C(=O)[O-]) `REAL300004919241.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.0.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.0.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.0.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919241 none CC#CCC(NC(=O)C(NC(=O)OC(C)(C)C)C(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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: [13, 13, 13, 7, 3, 3, 1, 3, 1, 1, 4, 7, 7, 7, 7, 7, 7, 1, 2, 2, 2, 7, 9, 9, 13, 13, 13, 13, 13, 7, 3, 1, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2] 31 rigid atoms, others: [8, 9, 31, 6, 17] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 86 number of broken/clashed sets: 0 ./output.0.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919241 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919241 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919241/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919241 Building REAL300004919242 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919242' /scratch/stefan/7775247/working/building/REAL300004919242 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919242 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919242/0 /scratch/stefan/7775247/working/building/REAL300004919242 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/242 `/scratch/stefan/7775247/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(C)N=C1C1CCCCC1)C(=O)[O-]) `REAL300004919242.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919242 none CC#CCC(NC(=O)C1=CN(C)N=C1C1CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 8, 5, 8, 1, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 45, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 45, 71, 71, 102, 102, 102, 102, 102, 45, 12, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 186 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 30] set([0, 1, 2, 3, 4, 5, 7, 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]) total number of confs: 516 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: REAL300004919242 none CC#CCC(NC(=O)C1=CN(C)N=C1C1CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 8, 5, 8, 1, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [188, 188, 188, 101, 44, 44, 6, 44, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 101, 130, 130, 188, 188, 188, 188, 188, 101, 44, 6, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 188 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 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]) total number of confs: 851 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919242 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919242 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919242/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919242 Building REAL300004919243 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919243' /scratch/stefan/7775247/working/building/REAL300004919243 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919243 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919243/0 /scratch/stefan/7775247/working/building/REAL300004919243 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 243) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/243 `/scratch/stefan/7775247/working/3D/243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC([N+](=O)[O-])=CC2=C1OCCO2)C(=O)[O-]) `REAL300004919243.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919243 none CC#CCC(NC(=O)C1=CC([N+](=O)[O-])=CC2=C1OCCO2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 8, 11, 11, 1, 1, 1, 12, 5, 5, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 3, 7, 2, 2, 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: [83, 83, 83, 33, 12, 12, 1, 12, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 33, 49, 49, 83, 83, 83, 83, 83, 33, 12, 1, 1, 1, 1, 1, 1] 83 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 396 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919243 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919243 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919243/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919243 Building REAL300004919244 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919244' /scratch/stefan/7775247/working/building/REAL300004919244 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919244 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919244/0 /scratch/stefan/7775247/working/building/REAL300004919244 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/244 `/scratch/stefan/7775247/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)C=CC=C1I)C(=O)[O-]) `REAL300004919244.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919244 none CC#CCC(NC(=O)C1=C(C)C=CC=C1I)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 1, 1, 1, 1, 18, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 24, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 24, 34, 34, 47, 47, 47, 47, 47, 24, 6, 2, 2, 2, 1, 1, 1] 47 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919244 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919244 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919244/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919244 Building REAL300004919245 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919245' /scratch/stefan/7775247/working/building/REAL300004919245 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919245 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919245/0 /scratch/stefan/7775247/working/building/REAL300004919245 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/245 `/scratch/stefan/7775247/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CN(C)C2=CC=CC=C12)C(=O)[O-]) `REAL300004919245.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919245 none CC#CCC(NC(=O)CCC1=CN(C)C2=CC=CC=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 5, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 55, 39, 39, 10, 39, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 56, 56, 77, 77, 77, 77, 77, 55, 39, 10, 10, 5, 5, 1, 2, 2, 2, 1, 1, 1, 1] 77 rigid atoms, others: [34, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37]) total number of confs: 327 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919245 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919245 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919245/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919245 Building REAL300004919246 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919246' /scratch/stefan/7775247/working/building/REAL300004919246 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919246 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919246/0 /scratch/stefan/7775247/working/building/REAL300004919246 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/246 `/scratch/stefan/7775247/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC(CC1=CC=CC=C1)NC(=O)OC(C)(C)C)C(=O)[O-]) `REAL300004919246.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919246 none CC#CCC(NC(=O)CC(CC1=CC=CC=C1)NC(=O)OC(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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: [61, 61, 61, 33, 22, 22, 13, 22, 6, 2, 1, 1, 1, 1, 1, 1, 1, 6, 16, 25, 25, 41, 42, 42, 42, 33, 44, 44, 61, 61, 61, 61, 61, 33, 22, 13, 13, 6, 2, 2, 1, 1, 1, 1, 1, 16, 42, 42, 42, 42, 42, 42, 42, 42, 42] 165 rigid atoms, others: [43, 40, 41, 10, 11, 12, 13, 14, 15, 16, 44, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 407 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919246 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919246 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919246/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919246 Building REAL300004919247 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919247' /scratch/stefan/7775247/working/building/REAL300004919247 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919247 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919247/0 /scratch/stefan/7775247/working/building/REAL300004919247 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 247) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/247 `/scratch/stefan/7775247/working/3D/247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1CN(C(=O)OC(C)(C)C)C1)C(=O)[O-]) `REAL300004919247.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919247 none CC#CCC(NC(=O)COC1CN(C(=O)OC(C)(C)C)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [49, 49, 49, 38, 29, 29, 14, 29, 6, 1, 1, 1, 1, 1, 2, 2, 10, 12, 12, 12, 1, 38, 44, 44, 49, 49, 49, 49, 49, 38, 29, 14, 14, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1] 118 rigid atoms, others: [33, 34, 35, 9, 10, 11, 12, 13, 46, 45, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 276 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919247 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919247 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919247/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919247 Building REAL300004919248 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919248' /scratch/stefan/7775247/working/building/REAL300004919248 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919248 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919248/0 /scratch/stefan/7775247/working/building/REAL300004919248 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/248 `/scratch/stefan/7775247/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CC)OC1=CC=CC=C1Cl)C(=O)[O-]) `REAL300004919248.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919248 none CC#CCC(NC(=O)C(CC)OC1=CC=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 16, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [176, 176, 176, 86, 45, 45, 13, 45, 6, 13, 23, 1, 1, 1, 1, 1, 1, 1, 1, 86, 125, 125, 176, 176, 176, 176, 176, 86, 45, 13, 25, 25, 25, 25, 25, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 952 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919248 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919248 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919248/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919248 Building REAL300004919249 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919249' /scratch/stefan/7775247/working/building/REAL300004919249 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919249 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919249/0 /scratch/stefan/7775247/working/building/REAL300004919249 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/249 `/scratch/stefan/7775247/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=C(OC)C=C1Cl)C(=O)[O-]) `REAL300004919249.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919249 none CC#CCC(NC(=O)CC1=CC=C(OC)C=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 12, 5, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [153, 153, 153, 65, 33, 33, 6, 33, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 65, 111, 111, 153, 153, 153, 153, 153, 65, 33, 6, 6, 1, 1, 3, 3, 3, 1] 201 rigid atoms, others: [35, 8, 9, 10, 11, 12, 13, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 833 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919249 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919249 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919249/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919249 Building REAL300004919250 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919250' /scratch/stefan/7775247/working/building/REAL300004919250 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919250 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919250/0 /scratch/stefan/7775247/working/building/REAL300004919250 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/250 `/scratch/stefan/7775247/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC=C2CCCCC2=C1)C(=O)[O-]) `REAL300004919250.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919250 none CC#CCC(NC(=O)COC1=CC=C2CCCCC2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [137, 137, 137, 121, 81, 81, 22, 81, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 121, 127, 127, 137, 137, 137, 137, 137, 121, 81, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 137 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 550 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919250 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919250 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919250/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919250 Building REAL300004919251 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919251' /scratch/stefan/7775247/working/building/REAL300004919251 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919251 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919251/0 /scratch/stefan/7775247/working/building/REAL300004919251 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 251) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/251 `/scratch/stefan/7775247/working/3D/251' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)CSC1=CC=C(F)C=C1)C(=O)[O-]) `REAL300004919251.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919251 none CC#CCC(NC(=O)C(C)CSC1=CC=C(F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 5, 14, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [87, 87, 87, 76, 49, 49, 17, 49, 11, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 76, 80, 80, 87, 87, 87, 87, 87, 76, 49, 17, 17, 17, 17, 11, 11, 1, 1, 1, 1] 87 rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 375 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919251 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919251 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919251/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919251 Building REAL300004919252 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919252' /scratch/stefan/7775247/working/building/REAL300004919252 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919252 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919252/0 /scratch/stefan/7775247/working/building/REAL300004919252 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/252 `/scratch/stefan/7775247/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CC)CC1=CC=CC=C1Br)C(=O)[O-]) `REAL300004919252.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919252 none CC#CCC(NC(=O)C(CC)CC1=CC=CC=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [190, 190, 190, 92, 43, 43, 11, 43, 6, 11, 15, 1, 1, 1, 1, 1, 1, 1, 1, 92, 128, 128, 190, 190, 190, 190, 190, 92, 43, 11, 15, 15, 15, 15, 15, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 950 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919252 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919252 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919252/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919252 Building REAL300004919253 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919253' /scratch/stefan/7775247/working/building/REAL300004919253 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919253 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919253/0 /scratch/stefan/7775247/working/building/REAL300004919253 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/253 `/scratch/stefan/7775247/working/3D/253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(CC2=CC=CC(F)=C2)N=N1)C(=O)[O-]) `REAL300004919253.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919253 none CC#CCC(NC(=O)C1=CN(CC2=CC=CC(F)=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 1, 1, 15, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 5, 5, 1, 5, 1, 1, 1, 1, 8, 29, 29, 29, 29, 29, 29, 1, 1, 13, 20, 20, 31, 31, 31, 31, 31, 13, 5, 1, 8, 8, 29, 29, 29, 29] 201 rigid atoms, others: [6, 8, 9, 10, 11, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37]) 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: REAL300004919253 none CC#CCC(NC(=O)C1=CN(CC2=CC=CC(F)=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 1, 1, 15, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 66, 66, 29, 66, 29, 29, 6, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 116, 154, 154, 201, 201, 201, 201, 201, 116, 66, 29, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 965 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919253 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919253 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919253/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919253 Building REAL300004919254 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919254' /scratch/stefan/7775247/working/building/REAL300004919254 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919254 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919254/0 /scratch/stefan/7775247/working/building/REAL300004919254 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/254 `/scratch/stefan/7775247/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CNC2=CC=C([N+](=O)[O-])C=C12)C(=O)[O-]) `REAL300004919254.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919254 none CC#CCC(NC(=O)CC1=CNC2=CC=C([N+](=O)[O-])C=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 97, 49, 49, 8, 49, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 97, 139, 139, 201, 201, 201, 201, 201, 97, 49, 8, 8, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 1007 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919254 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919254 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919254/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919254 Building REAL300004919255 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919255' /scratch/stefan/7775247/working/building/REAL300004919255 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919255 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919255/0 /scratch/stefan/7775247/working/building/REAL300004919255 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/255 `/scratch/stefan/7775247/working/3D/255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CC12CCCC1=CC=CC=C12)C(=O)[O-]) `REAL300004919255.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919255 none CC#CCC(NC(=O)C1CC12CCCC1=CC=CC=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 36, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 49, 49, 72, 72, 72, 72, 72, 36, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 72 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 331 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919255 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919255 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919255/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919255 Building REAL300004919256 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919256' /scratch/stefan/7775247/working/building/REAL300004919256 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919256 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919256/0 /scratch/stefan/7775247/working/building/REAL300004919256 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/256 `/scratch/stefan/7775247/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C2=CC=C(F)C=C2)=C(C)S1)C(=O)[O-]) `REAL300004919256.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919256 none CC#CCC(NC(=O)C1=CC(C2=CC=C(F)C=C2)=C(C)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 5, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [126, 126, 126, 49, 12, 12, 1, 12, 1, 1, 1, 1, 4, 4, 1, 1, 4, 4, 1, 1, 1, 49, 74, 74, 126, 126, 126, 126, 126, 49, 13, 1, 4, 4, 4, 4, 1, 1, 1] 130 rigid atoms, others: [36, 37, 6, 8, 9, 10, 11, 18, 19, 20, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35]) total number of confs: 598 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919256 none CC#CCC(NC(=O)C1=CC(C2=CC=C(F)C=C2)=C(C)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 5, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [130, 130, 130, 76, 36, 36, 4, 36, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 76, 93, 93, 130, 130, 130, 130, 130, 76, 36, 4, 1, 1, 1, 1, 4, 4, 4] 130 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 581 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919256 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919256 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919256/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919256 Building REAL300004919257 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919257' /scratch/stefan/7775247/working/building/REAL300004919257 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919257 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919257/0 /scratch/stefan/7775247/working/building/REAL300004919257 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/257 `/scratch/stefan/7775247/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(N2C=CC(C(F)(F)F)=N2)=C1)C(=O)[O-]) `REAL300004919257.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919257 none CC#CCC(NC(=O)C1=CC=CC(N2C=CC(C(F)(F)F)=N2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 1, 1, 5, 15, 15, 15, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 24, 42, 42, 80, 80, 80, 80, 80, 24, 7, 1, 1, 1, 7, 7, 1] 201 rigid atoms, others: [33, 34, 35, 38, 6, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37]) total number of confs: 382 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919257 none CC#CCC(NC(=O)C1=CC=CC(N2C=CC(C(F)(F)F)=N2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 1, 1, 5, 15, 15, 15, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 87, 27, 27, 7, 27, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 7, 87, 120, 120, 201, 201, 201, 201, 201, 87, 27, 7, 7, 7, 1, 1, 7] 201 rigid atoms, others: [36, 37, 12, 13, 14, 15, 16, 17, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 963 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919257 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919257 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919257/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919257 Building REAL300004919258 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919258' /scratch/stefan/7775247/working/building/REAL300004919258 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919258 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919258/0 /scratch/stefan/7775247/working/building/REAL300004919258 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/258 `/scratch/stefan/7775247/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C(F)F)N(CC(C)C)N=C1)C(=O)[O-]) `REAL300004919258.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919258 none CC#CCC(NC(=O)C1=C(C(F)F)N(CC(C)C)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 5, 15, 15, 8, 5, 5, 5, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 43, 11, 11, 1, 11, 1, 1, 1, 7, 7, 1, 1, 4, 5, 5, 1, 1, 43, 67, 67, 118, 118, 118, 118, 118, 43, 11, 7, 4, 4, 5, 5, 5, 5, 5, 5, 5, 1] 201 rigid atoms, others: [6, 8, 9, 10, 13, 14, 40, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 587 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919258 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919258 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919258/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919258 Building REAL300004919259 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919259' /scratch/stefan/7775247/working/building/REAL300004919259 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919259 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919259/0 /scratch/stefan/7775247/working/building/REAL300004919259 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/259 `/scratch/stefan/7775247/working/3D/259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=NN(C2=CC=CC=C2)C=C1)C(=O)[O-]) `REAL300004919259.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919259 none CC#CCC(NC(=O)CC1=NN(C2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 192, 97, 43, 43, 7, 43, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 1, 97, 139, 139, 192, 192, 192, 192, 192, 97, 43, 7, 7, 4, 4, 2, 4, 4, 1, 1] 201 rigid atoms, others: [37, 38, 8, 9, 10, 11, 12, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 970 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919259 none CC#CCC(NC(=O)CC1=NN(C2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 108, 55, 55, 14, 55, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 108, 149, 149, 201, 201, 201, 201, 201, 108, 55, 14, 14, 1, 1, 1, 1, 1, 4, 4] 201 rigid atoms, others: [32, 33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38]) total number of confs: 1003 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919259 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919259 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919259/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919259 Building REAL300004919260 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919260' /scratch/stefan/7775247/working/building/REAL300004919260 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919260 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919260/0 /scratch/stefan/7775247/working/building/REAL300004919260 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/260 `/scratch/stefan/7775247/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)S(=O)(=O)C1CCOCC1)C(=O)[O-]) `REAL300004919260.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919260 none CC#CCC(NC(=O)C(C)S(=O)(=O)C1CCOCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 14, 11, 11, 5, 5, 5, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 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: [104, 104, 104, 60, 28, 28, 8, 28, 4, 8, 1, 4, 4, 1, 1, 1, 1, 1, 1, 60, 76, 76, 104, 104, 104, 104, 104, 60, 28, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1] 104 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 10, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 486 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919260 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919260 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919260/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919260 Building REAL300004919261 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919261' /scratch/stefan/7775247/working/building/REAL300004919261 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919261 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919261/0 /scratch/stefan/7775247/working/building/REAL300004919261 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/261 `/scratch/stefan/7775247/working/3D/261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(CC2=CC=CC=C2)CC2CCC1C2)C(=O)[O-]) `REAL300004919261.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919261 none CC#CCC(NC(=O)C1(CC2=CC=CC=C2)CC2CCC1C2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [14, 14, 14, 5, 2, 2, 1, 2, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 8, 8, 14, 14, 14, 14, 14, 5, 2, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 23 rigid atoms, others: [48, 6, 39, 8, 9, 41, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 40, 42] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 83 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919261 none CC#CCC(NC(=O)C1(CC2=CC=CC=C2)CC2CCC1C2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 12, 5, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 12, 13, 13, 23, 23, 23, 23, 23, 12, 5, 2, 2, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 23 rigid atoms, others: [34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 106 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919261 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919261 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919261/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919261 Building REAL300004919262 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919262' /scratch/stefan/7775247/working/building/REAL300004919262 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919262 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919262/0 /scratch/stefan/7775247/working/building/REAL300004919262 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/262 `/scratch/stefan/7775247/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)CC1=CC=C(F)C(Br)=C1)C(=O)[O-]) `REAL300004919262.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919262 none CC#CCC(NC(=O)C(C)CC1=CC=C(F)C(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 15, 1, 17, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 108, 48, 48, 9, 48, 3, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 108, 146, 146, 201, 201, 201, 201, 201, 108, 48, 9, 9, 9, 9, 3, 3, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 994 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919262 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919262 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919262/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919262 Building REAL300004919263 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919263' /scratch/stefan/7775247/working/building/REAL300004919263 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919263 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919263/0 /scratch/stefan/7775247/working/building/REAL300004919263 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/263 `/scratch/stefan/7775247/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CN(C)C2=CC=CC=C12)C(=O)[O-]) `REAL300004919263.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919263 none CC#CCC(NC(=O)C=CC1=CN(C)C2=CC=CC=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 64, 64, 11, 64, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 116, 149, 149, 201, 201, 201, 201, 201, 116, 64, 11, 11, 1, 2, 2, 2, 1, 1, 1, 1] 201 rigid atoms, others: [32, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 931 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919263 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919263 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919263/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919263 Building REAL300004919264 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919264' /scratch/stefan/7775247/working/building/REAL300004919264 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919264 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919264/0 /scratch/stefan/7775247/working/building/REAL300004919264 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/264 `/scratch/stefan/7775247/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1(NC(=O)OC(C)(C)C)CCC1)C(=O)[O-]) `REAL300004919264.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919264 none CC#CCC(NC(=O)CC1(NC(=O)OC(C)(C)C)CCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 4, 7, 6, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 6, 5, 5, 3, 5, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 6, 5, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1] 11 rigid atoms, others: [8, 9, 10, 43, 44, 45, 46, 47, 48, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919264 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919264 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919264/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919264 Building REAL300004919265 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919265' /scratch/stefan/7775247/working/building/REAL300004919265 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919265 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919265/0 /scratch/stefan/7775247/working/building/REAL300004919265 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/265 `/scratch/stefan/7775247/working/3D/265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC=C(Br)C(C)=C1)C(=O)[O-]) `REAL300004919265.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919265 none CC#CCC(NC(=O)CCC1=CC=C(Br)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 1, 1, 1, 1, 17, 1, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 104, 57, 57, 12, 56, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 104, 141, 141, 201, 201, 201, 201, 201, 104, 57, 12, 12, 8, 8, 1, 1, 2, 2, 2, 1] 201 rigid atoms, others: [32, 33, 37, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 967 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919265 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919265 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919265/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919265 Building REAL300004919266 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919266' /scratch/stefan/7775247/working/building/REAL300004919266 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919266 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919266/0 /scratch/stefan/7775247/working/building/REAL300004919266 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/266 `/scratch/stefan/7775247/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(F)C=C1OC(F)F)C(=O)[O-]) `REAL300004919266.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919266 none CC#CCC(NC(=O)C1=CC=C(F)C=C1OC(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 12, 5, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 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, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 1, 1, 1, 5] 5 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 32, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 28 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919266 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919266 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919266/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919266 Building REAL300004919267 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919267' /scratch/stefan/7775247/working/building/REAL300004919267 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919267 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919267/0 /scratch/stefan/7775247/working/building/REAL300004919267 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/267 `/scratch/stefan/7775247/working/3D/267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=C(Br)C=C2)C(C)=C1)C(=O)[O-]) `REAL300004919267.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919267 none CC#CCC(NC(=O)C1=NN(C2=CC=C(Br)C=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [97, 97, 97, 32, 11, 11, 1, 11, 1, 1, 1, 1, 5, 5, 1, 3, 5, 5, 1, 1, 1, 32, 51, 51, 97, 97, 97, 97, 97, 32, 11, 5, 5, 5, 5, 2, 2, 2, 1] 125 rigid atoms, others: [38, 6, 8, 9, 10, 11, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 467 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: REAL300004919267 none CC#CCC(NC(=O)C1=NN(C2=CC=C(Br)C=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 125, 58, 24, 24, 5, 24, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 58, 82, 82, 125, 125, 125, 125, 125, 58, 24, 1, 1, 1, 1, 5, 5, 5, 5] 125 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 585 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919267 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919267 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919267/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919267 Building REAL300004919268 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919268' /scratch/stefan/7775247/working/building/REAL300004919268 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919268 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919268/0 /scratch/stefan/7775247/working/building/REAL300004919268 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/268 `/scratch/stefan/7775247/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCOC1=CC=C(C)C(C)=C1)C(=O)[O-]) `REAL300004919268.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919268 none CC#CCC(NC(=O)CCCOC1=CC=C(C)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 5, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 129, 129, 48, 129, 30, 10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 180, 181, 181, 201, 201, 201, 201, 201, 180, 129, 48, 48, 30, 30, 10, 10, 1, 1, 2, 2, 2, 2, 2, 2, 1] 201 rigid atoms, others: [36, 37, 44, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43]) total number of confs: 903 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919268 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919268 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919268/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919268 Building REAL300004919269 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919269' /scratch/stefan/7775247/working/building/REAL300004919269 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919269 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919269/0 /scratch/stefan/7775247/working/building/REAL300004919269 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/269 `/scratch/stefan/7775247/working/3D/269' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)CN(C)C(=O)OC(C)(C)C)C(=O)[O-]) `REAL300004919269.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.0.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.0.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.0.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919269 none CC#CCC(NC(=O)C(C)CN(C)C(=O)OC(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 8, 5, 1, 11, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 3, 4, 4, 6, 6, 8, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 2, 2, 2, 3, 3, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8] 8 rigid atoms, others: [8, 9, 10, 30, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 40 number of broken/clashed sets: 0 ./output.0.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919269 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919269 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919269/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919269 Building REAL300004919270 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919270' /scratch/stefan/7775247/working/building/REAL300004919270 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919270 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919270/0 /scratch/stefan/7775247/working/building/REAL300004919270 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/270 `/scratch/stefan/7775247/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Cl)=CC=C1SCC)C(=O)[O-]) `REAL300004919270.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919270 none CC#CCC(NC(=O)C1=CC(Cl)=CC=C1SCC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 1, 1, 14, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 30, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 9, 28, 30, 48, 48, 85, 85, 85, 85, 85, 30, 11, 1, 1, 1, 28, 28, 29, 29, 29] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 497 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919270 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919270 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919270/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919270 Building REAL300004919271 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919271' /scratch/stefan/7775247/working/building/REAL300004919271 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919271 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919271/0 /scratch/stefan/7775247/working/building/REAL300004919271 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 271) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/271 `/scratch/stefan/7775247/working/3D/271' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C(C)C)N1CCCS1(=O)=O)C(=O)[O-]) `REAL300004919271.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919271 none CC#CCC(NC(=O)C(C(C)C)N1CCCS1(=O)=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 8, 5, 5, 5, 14, 11, 11, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 14, 9, 9, 3, 9, 1, 3, 6, 6, 1, 1, 1, 1, 1, 1, 1, 14, 18, 18, 24, 24, 24, 24, 24, 14, 9, 3, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1] 24 rigid atoms, others: [17, 37, 38, 39, 8, 41, 42, 12, 13, 14, 15, 16, 40, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 137 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919271 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919271 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919271/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919271 Building REAL300004919272 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919272' /scratch/stefan/7775247/working/building/REAL300004919272 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919272 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919272/0 /scratch/stefan/7775247/working/building/REAL300004919272 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/272 `/scratch/stefan/7775247/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=C(Cl)C(Cl)=C2)CCC1)C(=O)[O-]) `REAL300004919272.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919272 none CC#CCC(NC(=O)C1(C2=CC=C(Cl)C(Cl)=C2)CCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 98, 36, 11, 11, 1, 11, 1, 1, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 36, 56, 56, 98, 98, 98, 98, 98, 36, 11, 9, 9, 9, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 17, 18, 19, 38] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 472 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: REAL300004919272 none CC#CCC(NC(=O)C1(C2=CC=C(Cl)C(Cl)=C2)CCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 1, 1, 1, 1, 16, 1, 16, 1, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 98, 45, 45, 9, 45, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 98, 135, 135, 201, 201, 201, 201, 201, 98, 45, 1, 1, 1, 9, 9, 9, 9, 9, 9] 201 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 951 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919272 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919272 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919272/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919272 Building REAL300004919273 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919273' /scratch/stefan/7775247/working/building/REAL300004919273 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919273 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919273/0 /scratch/stefan/7775247/working/building/REAL300004919273 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 273) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/273 `/scratch/stefan/7775247/working/3D/273' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC)C=C1I)C(=O)[O-]) `REAL300004919273.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919273 none CC#CCC(NC(=O)C1=CC=C(OC)C=C1I)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'I', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 18, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 2, 1, 1, 1, 24, 37, 37, 62, 62, 62, 62, 62, 24, 7, 1, 1, 3, 3, 3, 1] 98 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 14, 15, 16, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 300 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919273 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919273 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919273/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919273 Building REAL300004919274 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919274' /scratch/stefan/7775247/working/building/REAL300004919274 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919274 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919274/0 /scratch/stefan/7775247/working/building/REAL300004919274 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/274 `/scratch/stefan/7775247/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)(C)CNC(=O)OC(C)(C)C)C(=O)[O-]) `REAL300004919274.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.0.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.0.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.0.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919274 none CC#CCC(NC(=O)C(C)(C)CNC(=O)OC(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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: [13, 13, 13, 8, 3, 3, 1, 3, 1, 1, 1, 1, 4, 7, 10, 10, 11, 12, 12, 12, 8, 11, 11, 13, 13, 13, 13, 13, 8, 3, 2, 2, 2, 2, 2, 2, 4, 4, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12] 31 rigid atoms, others: [8, 9, 10, 11, 6] set([0, 1, 2, 3, 4, 5, 7, 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: 115 number of broken/clashed sets: 0 ./output.0.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919274 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919274 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919274/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919274 Building REAL300004919275 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919275' /scratch/stefan/7775247/working/building/REAL300004919275 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919275 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919275/0 /scratch/stefan/7775247/working/building/REAL300004919275 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 275) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/275 `/scratch/stefan/7775247/working/3D/275' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CNC2=CC=C(C)C=C12)C(=O)[O-]) `REAL300004919275.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919275 none CC#CCC(NC(=O)CCC1=CNC2=CC=C(C)C=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 5, 1, 1, 8, 1, 1, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 56, 39, 39, 10, 39, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 56, 57, 57, 81, 81, 81, 81, 81, 56, 39, 10, 10, 5, 5, 1, 1, 1, 1, 2, 2, 2, 1] 81 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40]) total number of confs: 351 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919275 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919275 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919275/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919275 Building REAL300004919276 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919276' /scratch/stefan/7775247/working/building/REAL300004919276 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919276 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919276/0 /scratch/stefan/7775247/working/building/REAL300004919276 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/276 `/scratch/stefan/7775247/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)(C)CC1=CC=CC(Cl)=C1)C(=O)[O-]) `REAL300004919276.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919276 none CC#CCC(NC(=O)C(C)(C)CC1=CC=CC(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 105, 43, 43, 16, 43, 3, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 105, 143, 143, 201, 201, 201, 201, 201, 105, 43, 16, 16, 16, 16, 16, 16, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 1007 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919276 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919276 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919276/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919276 Building REAL300004919277 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919277' /scratch/stefan/7775247/working/building/REAL300004919277 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919277 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919277/0 /scratch/stefan/7775247/working/building/REAL300004919277 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/277 `/scratch/stefan/7775247/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CC)C1=CC=CC(C(F)(F)F)=C1)C(=O)[O-]) `REAL300004919277.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919277 none CC#CCC(NC(=O)C(CC)C1=CC=CC(C(F)(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [180, 180, 180, 79, 39, 38, 12, 39, 1, 12, 17, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 79, 127, 127, 180, 180, 180, 180, 180, 79, 38, 12, 17, 17, 17, 17, 17, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 8, 11, 12, 13, 14, 15, 16, 40, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 981 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919277 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919277 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919277/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919277 Building REAL300004919278 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919278' /scratch/stefan/7775247/working/building/REAL300004919278 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919278 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919278/0 /scratch/stefan/7775247/working/building/REAL300004919278 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/278 `/scratch/stefan/7775247/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)C1=CC=C(OC)C(OC)=C1)C(=O)[O-]) `REAL300004919278.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919278 none CC#CCC(NC(=O)C(C)C1=CC=C(OC)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 119, 56, 29, 28, 8, 28, 1, 8, 1, 1, 1, 1, 1, 3, 1, 1, 3, 1, 56, 84, 84, 119, 119, 119, 119, 119, 56, 28, 8, 9, 9, 9, 1, 1, 4, 4, 4, 4, 4, 4, 1] 201 rigid atoms, others: [34, 35, 8, 10, 11, 12, 13, 14, 16, 17, 19, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 619 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919278 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919278 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919278/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919278 Building REAL300004919279 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919279' /scratch/stefan/7775247/working/building/REAL300004919279 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919279 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919279/0 /scratch/stefan/7775247/working/building/REAL300004919279 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/279 `/scratch/stefan/7775247/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=CC(C)=CC=C2C)N=C1)C(=O)[O-]) `REAL300004919279.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919279 none CC#CCC(NC(=O)C1=C(C)N(C2=CC(C)=CC=C2C)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 5, 1, 1, 1, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [121, 121, 121, 48, 12, 12, 1, 12, 1, 1, 1, 1, 1, 6, 6, 6, 2, 6, 6, 6, 1, 1, 48, 78, 78, 121, 121, 121, 121, 121, 48, 12, 2, 2, 2, 6, 6, 6, 6, 5, 6, 6, 6, 6, 1] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 44, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 632 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919279 none CC#CCC(NC(=O)C1=C(C)N(C2=CC(C)=CC=C2C)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 5, 1, 1, 1, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 115, 47, 47, 6, 47, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 115, 150, 150, 201, 201, 201, 201, 201, 115, 47, 6, 6, 6, 1, 2, 2, 2, 1, 1, 2, 2, 2, 6] 201 rigid atoms, others: [35, 39, 40, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 957 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919279 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919279 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919279/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919279 Building REAL300004919280 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919280' /scratch/stefan/7775247/working/building/REAL300004919280 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919280 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919280/0 /scratch/stefan/7775247/working/building/REAL300004919280 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/280 `/scratch/stefan/7775247/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=C(C)C1=CC=CC=C1OC(F)F)C(=O)[O-]) `REAL300004919280.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919280 none CC#CCC(NC(=O)C=C(C)C1=CC=CC=C1OC(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [135, 135, 135, 64, 40, 40, 7, 40, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 64, 98, 98, 135, 135, 135, 135, 135, 64, 40, 7, 7, 7, 7, 1, 1, 1, 1, 15] 201 rigid atoms, others: [35, 36, 37, 38, 9, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39]) total number of confs: 747 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919280 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919280 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919280/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919280 Building REAL300004919281 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919281' /scratch/stefan/7775247/working/building/REAL300004919281 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919281 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919281/0 /scratch/stefan/7775247/working/building/REAL300004919281 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/281 `/scratch/stefan/7775247/working/3D/281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Cl)=CC=C1OC1CCCC1)C(=O)[O-]) `REAL300004919281.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919281 none CC#CCC(NC(=O)C1=CC(Cl)=CC=C1OC1CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 30, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 8, 22, 22, 22, 22, 30, 48, 48, 84, 84, 84, 84, 84, 30, 12, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 450 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919281 none CC#CCC(NC(=O)C1=CC(Cl)=CC=C1OC1CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 124, 86, 86, 22, 86, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 1, 1, 124, 153, 153, 201, 201, 201, 201, 201, 124, 86, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 882 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919281 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919281 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919281/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919281 Building REAL300004919282 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919282' /scratch/stefan/7775247/working/building/REAL300004919282 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919282 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919282/0 /scratch/stefan/7775247/working/building/REAL300004919282 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/282 `/scratch/stefan/7775247/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCC1=CSC2=CC=CC=C12)C(=O)[O-]) `REAL300004919282.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919282 none CC#CCC(NC(=O)CCCC1=CSC2=CC=CC=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 102, 49, 49, 11, 49, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 102, 148, 148, 201, 201, 201, 201, 201, 102, 49, 11, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 40, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 1061 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919282 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919282 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919282/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919282 Building REAL300004919283 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919283' /scratch/stefan/7775247/working/building/REAL300004919283 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919283 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919283/0 /scratch/stefan/7775247/working/building/REAL300004919283 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/283 `/scratch/stefan/7775247/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC(OC)=CC=C1Br)C(=O)[O-]) `REAL300004919283.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919283 none CC#CCC(NC(=O)CC1=CC(OC)=CC=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 12, 5, 1, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [153, 153, 153, 73, 38, 38, 6, 38, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 73, 106, 106, 153, 153, 153, 153, 153, 73, 38, 6, 6, 1, 3, 3, 3, 1, 1] 201 rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 747 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919283 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919283 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919283/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919283 Building REAL300004919284 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919284' /scratch/stefan/7775247/working/building/REAL300004919284 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919284 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919284/0 /scratch/stefan/7775247/working/building/REAL300004919284 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/284 `/scratch/stefan/7775247/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCC1=C(Cl)SC(Cl)=C1)C(=O)[O-]) `REAL300004919284.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919284 none CC#CCC(NC(=O)CCCC1=C(Cl)SC(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'Cl', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 16, 14, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 98, 52, 52, 12, 52, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 98, 146, 146, 201, 201, 201, 201, 201, 98, 52, 12, 12, 5, 5, 5, 5, 1] 201 rigid atoms, others: [34, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 1059 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919284 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919284 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919284/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919284 Building REAL300004919285 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919285' /scratch/stefan/7775247/working/building/REAL300004919285 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919285 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919285/0 /scratch/stefan/7775247/working/building/REAL300004919285 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 285) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/285 `/scratch/stefan/7775247/working/3D/285' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(S(=O)(=O)N(C)C)=C(C)O1)C(=O)[O-]) `REAL300004919285.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919285 none CC#CCC(NC(=O)C1=CC(S(=O)(=O)N(C)C)=C(C)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 5, 12, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 37, 11, 11, 1, 11, 1, 1, 1, 1, 5, 5, 5, 9, 9, 1, 1, 1, 37, 57, 57, 102, 102, 102, 102, 102, 37, 11, 1, 9, 9, 9, 9, 9, 9, 2, 2, 2] 201 rigid atoms, others: [6, 8, 9, 10, 11, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 505 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919285 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919285 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919285/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919285 Building REAL300004919286 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919286' /scratch/stefan/7775247/working/building/REAL300004919286 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919286 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919286/0 /scratch/stefan/7775247/working/building/REAL300004919286 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/286 `/scratch/stefan/7775247/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCNC(=O)OC(C)(C)C)C(=O)[O-]) `REAL300004919286.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.0.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.0.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.0.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919286 none CC#CCC(NC(=O)CCCNC(=O)OC(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [13, 13, 13, 6, 5, 5, 3, 5, 1, 1, 1, 2, 7, 10, 10, 10, 10, 10, 10, 6, 9, 9, 13, 13, 13, 13, 13, 6, 5, 3, 3, 1, 1, 2, 2, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10] 31 rigid atoms, others: [8, 9, 10, 32, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 96 number of broken/clashed sets: 0 ./output.0.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919286 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919286 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919286/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919286 Building REAL300004919287 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919287' /scratch/stefan/7775247/working/building/REAL300004919287 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919287 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919287/0 /scratch/stefan/7775247/working/building/REAL300004919287 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 287) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/287 `/scratch/stefan/7775247/working/3D/287' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCN(S(=O)(=O)C2=C(C)ON=C2C)CC1)C(=O)[O-]) `REAL300004919287.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919287 none CC#CCC(NC(=O)C1CCN(S(=O)(=O)C2=C(C)ON=C2C)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 8, 14, 11, 11, 1, 1, 5, 12, 8, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 22, 9, 9, 1, 9, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 9, 1, 1, 22, 34, 34, 44, 44, 44, 44, 44, 22, 9, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 45, 46, 47, 48, 22, 23, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44]) 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: REAL300004919287 none CC#CCC(NC(=O)C1CCN(S(=O)(=O)C2=C(C)ON=C2C)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 8, 14, 11, 11, 1, 1, 5, 12, 8, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 120, 56, 56, 9, 56, 9, 9, 9, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 9, 9, 120, 161, 161, 201, 201, 201, 201, 201, 120, 56, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9] 201 rigid atoms, others: [12, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 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, 46, 47, 48]) total number of confs: 1036 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919287 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919287 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919287/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919287 Building REAL300004919288 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919288' /scratch/stefan/7775247/working/building/REAL300004919288 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919288 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919288/0 /scratch/stefan/7775247/working/building/REAL300004919288 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/288 `/scratch/stefan/7775247/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(CNC(=O)OC(C)(C)C)C=C1)C(=O)[O-]) `REAL300004919288.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919288 none CC#CCC(NC(=O)C1=CC=C(CNC(=O)OC(C)(C)C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 6, 25, 44, 44, 46, 46, 46, 46, 1, 1, 7, 11, 11, 17, 17, 17, 17, 17, 7, 3, 1, 1, 6, 6, 25, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1] 201 rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 12, 47, 48, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919288 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919288 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919288/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919288 Building REAL300004919289 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919289' /scratch/stefan/7775247/working/building/REAL300004919289 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919289 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919289/0 /scratch/stefan/7775247/working/building/REAL300004919289 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/289 `/scratch/stefan/7775247/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C12CC3CC(C1)CC(C1=CC=C(OC)C=C1)(C3)C2)C(=O)[O-]) `REAL300004919289.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919289 none CC#CCC(NC(=O)C12CC3CC(C1)CC(C1=CC=C(OC)C=C1)(C3)C2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 21, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1, 7, 4, 4, 1, 1, 21, 36, 36, 72, 72, 72, 72, 72, 21, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 4, 4, 1, 1, 1, 1] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 53, 54, 55, 56] set([0, 1, 2, 3, 4, 5, 7, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46, 47, 48, 49, 50, 51, 52]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919289 none CC#CCC(NC(=O)C12CC3CC(C1)CC(C1=CC=C(OC)C=C1)(C3)C2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [154, 154, 154, 56, 19, 19, 4, 19, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 2, 1, 1, 4, 4, 56, 93, 93, 154, 154, 154, 154, 154, 56, 19, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 2, 2, 2, 1, 1, 4, 4, 4, 4] 201 rigid atoms, others: [51, 46, 15, 16, 17, 18, 19, 20, 22, 23, 52, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50, 53, 54, 55, 56]) total number of confs: 779 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919289 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919289 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919289/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919289 Building REAL300004919290 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919290' /scratch/stefan/7775247/working/building/REAL300004919290 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919290 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919290/0 /scratch/stefan/7775247/working/building/REAL300004919290 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/290 `/scratch/stefan/7775247/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC(Cl)=CC=C1OC)C(=O)[O-]) `REAL300004919290.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919290 none CC#CCC(NC(=O)CC1=CC(Cl)=CC=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 16, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [166, 166, 166, 78, 36, 36, 5, 36, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 78, 120, 120, 166, 166, 166, 166, 166, 78, 36, 5, 5, 1, 1, 1, 4, 4, 4] 201 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 857 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919290 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919290 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919290/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919290 Building REAL300004919291 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919291' /scratch/stefan/7775247/working/building/REAL300004919291 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919291 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919291/0 /scratch/stefan/7775247/working/building/REAL300004919291 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/291 `/scratch/stefan/7775247/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCN(S(=O)(=O)C2=CC=CS2)C1)C(=O)[O-]) `REAL300004919291.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919291 none CC#CCC(NC(=O)C1CCCN(S(=O)(=O)C2=CC=CS2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 14, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 17, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 6, 6, 6, 28, 28, 28, 28, 1, 17, 26, 26, 41, 41, 41, 41, 41, 17, 7, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 43, 21, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41]) 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: REAL300004919291 none CC#CCC(NC(=O)C1CCCN(S(=O)(=O)C2=CC=CS2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 14, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 123, 78, 78, 28, 78, 28, 28, 28, 28, 9, 1, 9, 9, 1, 1, 1, 1, 1, 28, 123, 159, 159, 201, 201, 201, 201, 201, 123, 78, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 28, 28] 201 rigid atoms, others: [39, 40, 41, 13, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43]) total number of confs: 962 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919291 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919291 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919291/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919291 Building REAL300004919292 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919292' /scratch/stefan/7775247/working/building/REAL300004919292 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919292 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919292/0 /scratch/stefan/7775247/working/building/REAL300004919292 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/292 `/scratch/stefan/7775247/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C1=CC=CC(Cl)=C1)C(C)C)C(=O)[O-]) `REAL300004919292.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919292 none CC#CCC(NC(=O)C(C1=CC=CC(Cl)=C1)C(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [152, 152, 152, 70, 30, 30, 7, 30, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 70, 99, 99, 152, 152, 152, 152, 152, 70, 30, 7, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13] 159 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 784 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919292 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919292 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919292/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919292 Building REAL300004919293 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919293' /scratch/stefan/7775247/working/building/REAL300004919293 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919293 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919293/0 /scratch/stefan/7775247/working/building/REAL300004919293 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 293) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/293 `/scratch/stefan/7775247/working/3D/293' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CN1N=NC(C2=CC=C(C)C=C2)=N1)C(=O)[O-]) `REAL300004919293.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919293 none CC#CCC(NC(=O)CN1N=NC(C2=CC=C(C)C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 8, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 8, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 145, 58, 58, 8, 58, 1, 1, 1, 1, 1, 1, 3, 3, 1, 2, 3, 3, 1, 145, 176, 176, 201, 201, 201, 201, 201, 145, 58, 8, 8, 3, 3, 4, 4, 4, 3, 3] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 992 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919293 none CC#CCC(NC(=O)CN1N=NC(C2=CC=C(C)C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 8, 8, 8, 1, 1, 1, 1, 1, 5, 1, 1, 8, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 155, 78, 78, 17, 78, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 155, 184, 184, 201, 201, 201, 201, 201, 155, 78, 17, 17, 1, 1, 2, 2, 2, 1, 1] 201 rigid atoms, others: [33, 34, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 961 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919293 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919293 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919293/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919293 Building REAL300004919294 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919294' /scratch/stefan/7775247/working/building/REAL300004919294 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919294 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919294/0 /scratch/stefan/7775247/working/building/REAL300004919294 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/294 `/scratch/stefan/7775247/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CN1N=NC(C2=CC=C(Cl)C=C2)=N1)C(=O)[O-]) `REAL300004919294.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919294 none CC#CCC(NC(=O)CN1N=NC(C2=CC=C(Cl)C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 99, 52, 52, 8, 52, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 3, 1, 99, 143, 143, 200, 200, 200, 200, 200, 99, 52, 8, 8, 4, 4, 4, 4] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 1031 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919294 none CC#CCC(NC(=O)CN1N=NC(C2=CC=C(Cl)C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 78, 78, 22, 78, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 119, 154, 154, 201, 201, 201, 201, 201, 119, 78, 22, 21, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 956 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919294 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919294 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919294/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919294 Building REAL300004919295 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919295' /scratch/stefan/7775247/working/building/REAL300004919295 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919295 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919295/0 /scratch/stefan/7775247/working/building/REAL300004919295 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 295) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/295 `/scratch/stefan/7775247/working/3D/295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCN(C(=O)OC(C)(C)C)C1)C(=O)[O-]) `REAL300004919295.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919295 none CC#CCC(NC(=O)C1CCCN(C(=O)OC(C)(C)C)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 29, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 5, 5, 10, 12, 12, 12, 1, 29, 42, 42, 73, 73, 73, 73, 73, 29, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 47, 48, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 387 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919295 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919295 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919295/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919295 Building REAL300004919296 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919296' /scratch/stefan/7775247/working/building/REAL300004919296 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919296 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919296/0 /scratch/stefan/7775247/working/building/REAL300004919296 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/296 `/scratch/stefan/7775247/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC(C(C)=O)=C(C)O1)C(=O)[O-]) `REAL300004919296.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919296 none CC#CCC(NC(=O)CCC1=CC(C(C)=O)=C(C)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 5, 1, 1, 1, 1, 5, 11, 1, 5, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 2, 2, 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: [48, 48, 48, 32, 19, 19, 7, 19, 5, 1, 1, 1, 1, 1, 7, 7, 1, 1, 1, 32, 42, 42, 48, 48, 48, 48, 48, 32, 19, 7, 7, 5, 5, 1, 8, 8, 8, 2, 2, 2] 55 rigid atoms, others: [33, 9, 10, 11, 12, 13, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39]) total number of confs: 272 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919296 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919296 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919296/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919296 Building REAL300004919297 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919297' /scratch/stefan/7775247/working/building/REAL300004919297 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919297 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919297/0 /scratch/stefan/7775247/working/building/REAL300004919297 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/297 `/scratch/stefan/7775247/working/3D/297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(CC(F)(F)F)C(C)=C1)C(=O)[O-]) `REAL300004919297.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919297 none CC#CCC(NC(=O)C1=C(C)N(CC(F)(F)F)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 5, 8, 5, 5, 15, 15, 15, 1, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [95, 95, 95, 41, 12, 13, 1, 13, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 1, 41, 62, 62, 95, 95, 95, 95, 95, 41, 13, 2, 2, 2, 3, 3, 2, 2, 2, 1] 158 rigid atoms, others: [38, 6, 8, 9, 10, 11, 12, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 490 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919297 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919297 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919297/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919297 Building REAL300004919298 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919298' /scratch/stefan/7775247/working/building/REAL300004919298 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919298 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919298/0 /scratch/stefan/7775247/working/building/REAL300004919298 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/298 `/scratch/stefan/7775247/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1SCC1=CC=CO1)C(=O)[O-]) `REAL300004919298.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919298 none CC#CCC(NC(=O)C1=CC=CC=C1SCC1=CC=CO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 5, 1, 1, 1, 1, 12, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 7, 25, 34, 34, 34, 34, 19, 29, 29, 46, 46, 46, 46, 46, 19, 8, 1, 1, 1, 1, 25, 25, 34, 34, 34] 201 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39]) total number of confs: 311 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919298 none CC#CCC(NC(=O)C1=CC=CC=C1SCC1=CC=CO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 5, 1, 1, 1, 1, 12, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 125, 79, 80, 34, 80, 34, 34, 34, 34, 34, 18, 4, 1, 1, 1, 1, 1, 1, 125, 158, 158, 201, 201, 201, 201, 201, 125, 80, 34, 34, 34, 34, 4, 4, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 942 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919298 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919298 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919298/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919298 Building REAL300004919299 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919299' /scratch/stefan/7775247/working/building/REAL300004919299 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919299 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919299/0 /scratch/stefan/7775247/working/building/REAL300004919299 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/299 `/scratch/stefan/7775247/working/3D/299' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(S(=O)(=O)N2CCOCC2)=CN1C)C(=O)[O-]) `REAL300004919299.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919299 none CC#CCC(NC(=O)C1=CC(S(=O)(=O)N2CCOCC2)=CN1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 5, 5, 1, 5, 1, 1, 1, 1, 9, 9, 9, 39, 39, 39, 39, 39, 1, 1, 1, 12, 19, 19, 27, 27, 27, 27, 27, 12, 5, 1, 39, 39, 39, 39, 39, 39, 39, 39, 1, 2, 2, 2] 201 rigid atoms, others: [33, 6, 8, 9, 10, 11, 20, 21, 22, 42] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919299 none CC#CCC(NC(=O)C1=CC(S(=O)(=O)N2CCOCC2)=CN1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 1, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 146, 94, 94, 39, 94, 39, 39, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 39, 39, 39, 146, 173, 173, 201, 201, 201, 201, 201, 146, 94, 39, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 11, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42, 43, 44, 45]) total number of confs: 887 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919299 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919299 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919299/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919299 Building REAL300004919300 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919300' /scratch/stefan/7775247/working/building/REAL300004919300 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919300 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919300/0 /scratch/stefan/7775247/working/building/REAL300004919300 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/300 `/scratch/stefan/7775247/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=C(OC(C)C2)C(OC)=C1)C(=O)[O-]) `REAL300004919300.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919300 none CC#CCC(NC(=O)C1=CC2=C(OC(C)C2)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 5, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 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: [97, 97, 97, 30, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 30, 50, 50, 97, 97, 97, 97, 97, 30, 7, 1, 1, 2, 2, 2, 1, 1, 4, 4, 4, 1] 136 rigid atoms, others: [35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 40, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 37, 38, 39]) total number of confs: 464 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919300 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919300 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919300/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919300 Building REAL300004919301 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919301' /scratch/stefan/7775247/working/building/REAL300004919301 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919301 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919301/0 /scratch/stefan/7775247/working/building/REAL300004919301 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/301 `/scratch/stefan/7775247/working/3D/301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C#CC2=CC=CC=C2)C=C1)C(=O)[O-]) `REAL300004919301.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) Killed Solvation calculation failed Skipping REAL300004919301 0 /scratch/stefan/7775247/working/building/REAL300004919301 /scratch/stefan/7775247/working /scratch/stefan/7775247 `0' -> `0.failed' Finished preparing REAL300004919301 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Found failed protomers Marking REAL300004919301 as failed mkdir: created directory `/scratch/stefan/7775247/failed' `/scratch/stefan/7775247/working/building/REAL300004919301' -> `/scratch/stefan/7775247/failed/REAL300004919301' Building REAL300004919302 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919302' /scratch/stefan/7775247/working/building/REAL300004919302 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919302 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919302/0 /scratch/stefan/7775247/working/building/REAL300004919302 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/302 `/scratch/stefan/7775247/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1NC1=CC=C(C)C=C1)C(=O)[O-]) `REAL300004919302.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919302 none CC#CCC(NC(=O)C1=CC=CC=C1NC1=CC=C(C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 38, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 8, 8, 13, 13, 38, 64, 64, 108, 108, 108, 108, 108, 38, 12, 1, 1, 1, 1, 6, 13, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 7, 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]) total number of confs: 600 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: REAL300004919302 none CC#CCC(NC(=O)C1=CC=CC=C1NC1=CC=C(C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 76, 76, 13, 76, 13, 13, 13, 13, 13, 7, 1, 1, 1, 1, 1, 1, 1, 1, 137, 168, 168, 201, 201, 201, 201, 201, 137, 76, 13, 13, 13, 13, 7, 1, 1, 2, 2, 2, 1, 1] 201 rigid atoms, others: [37, 38, 42, 43, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 943 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919302 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919302 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919302/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919302 Building REAL300004919303 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919303' /scratch/stefan/7775247/working/building/REAL300004919303 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919303 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919303/0 /scratch/stefan/7775247/working/building/REAL300004919303 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 303) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/303 `/scratch/stefan/7775247/working/3D/303' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(CCC)C2=CC=C(OC)C=C21)C(=O)[O-]) `REAL300004919303.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919303 none CC#CCC(NC(=O)C1=C(C)N(CCC)C2=CC=C(OC)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 8, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 31, 13, 13, 1, 13, 1, 1, 1, 1, 1, 2, 5, 1, 1, 1, 1, 1, 2, 1, 1, 31, 47, 47, 83, 83, 83, 83, 83, 31, 13, 2, 2, 2, 2, 2, 6, 5, 6, 6, 6, 1, 1, 2, 2, 2, 1] 201 rigid atoms, others: [48, 43, 6, 8, 9, 10, 11, 12, 15, 16, 17, 18, 19, 21, 22, 44] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47]) total number of confs: 427 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919303 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919303 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919303/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919303 Building REAL300004919304 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919304' /scratch/stefan/7775247/working/building/REAL300004919304 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919304 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919304/0 /scratch/stefan/7775247/working/building/REAL300004919304 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/304 `/scratch/stefan/7775247/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC=C(C)C(Cl)=C1)C(=O)[O-]) `REAL300004919304.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919304 none CC#CCC(NC(=O)CCC1=CC=C(C)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 1, 1, 1, 1, 5, 1, 16, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 61, 31, 31, 6, 31, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 61, 76, 76, 94, 94, 94, 94, 94, 61, 31, 6, 6, 2, 2, 1, 1, 2, 2, 2, 1] 94 rigid atoms, others: [32, 33, 37, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 486 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919304 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919304 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919304/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919304 Building REAL300004919305 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919305' /scratch/stefan/7775247/working/building/REAL300004919305 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919305 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919305/0 /scratch/stefan/7775247/working/building/REAL300004919305 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 305) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/305 `/scratch/stefan/7775247/working/3D/305' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(S(=O)(=O)C2=CC=C(Cl)C=C2)CC1)C(=O)[O-]) `REAL300004919305.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919305 none CC#CCC(NC(=O)C1(S(=O)(=O)C2=CC=C(Cl)C=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 115, 44, 13, 13, 1, 13, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 44, 69, 69, 115, 115, 115, 115, 115, 44, 13, 7, 7, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 6, 8, 9, 19, 20, 38] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 565 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: REAL300004919305 none CC#CCC(NC(=O)C1(S(=O)(=O)C2=CC=C(Cl)C=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 11, 11, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 115, 45, 45, 7, 45, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 7, 7, 115, 147, 147, 201, 201, 201, 201, 201, 115, 45, 1, 1, 1, 1, 7, 7, 7, 7] 201 rigid atoms, others: [32, 33, 34, 9, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 955 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919305 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919305 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919305/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919305 Building REAL300004919306 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919306' /scratch/stefan/7775247/working/building/REAL300004919306 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919306 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919306/0 /scratch/stefan/7775247/working/building/REAL300004919306 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/306 `/scratch/stefan/7775247/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CC1C1=CC=C(C(F)(F)F)C=C1)C(=O)[O-]) `REAL300004919306.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919306 none CC#CCC(NC(=O)C1CC1C1=CC=C(C(F)(F)F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [129, 129, 129, 51, 13, 13, 1, 13, 1, 1, 1, 1, 7, 7, 1, 3, 7, 7, 7, 7, 7, 51, 80, 80, 129, 129, 129, 129, 129, 51, 13, 1, 1, 1, 1, 7, 7, 7, 7] 201 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 656 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: REAL300004919306 none CC#CCC(NC(=O)C1CC1C1=CC=C(C(F)(F)F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 124, 53, 53, 7, 53, 7, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 124, 151, 151, 201, 201, 201, 201, 201, 124, 53, 7, 7, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 917 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919306 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919306 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919306/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919306 Building REAL300004919307 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919307' /scratch/stefan/7775247/working/building/REAL300004919307 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919307 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919307/0 /scratch/stefan/7775247/working/building/REAL300004919307 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 307) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/307 `/scratch/stefan/7775247/working/3D/307' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1CC(C)CCC1C(C)C)C(=O)[O-]) `REAL300004919307.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919307 none CC#CCC(NC(=O)COC1CC(C)CCC1C(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [161, 161, 161, 94, 55, 55, 15, 55, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 94, 134, 134, 161, 161, 161, 161, 161, 94, 55, 15, 15, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5] 201 rigid atoms, others: [32, 33, 34, 35, 39, 40, 9, 10, 11, 12, 13, 14, 15, 16, 17, 43, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 866 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919307 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919307 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919307/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919307 Building REAL300004919308 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919308' /scratch/stefan/7775247/working/building/REAL300004919308 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919308 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919308/0 /scratch/stefan/7775247/working/building/REAL300004919308 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/308 `/scratch/stefan/7775247/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC=CC=C1C(C)CC)C(=O)[O-]) `REAL300004919308.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919308 none CC#CCC(NC(=O)COC1=CC=CC=C1C(C)CC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 153, 109, 109, 30, 109, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 153, 153, 153, 200, 200, 200, 200, 200, 153, 109, 30, 30, 1, 1, 1, 1, 2, 3, 3, 3, 4, 4, 4, 4, 4] 201 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16] 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, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 849 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919308 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919308 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919308/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919308 Building REAL300004919309 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919309' /scratch/stefan/7775247/working/building/REAL300004919309 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919309 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919309/0 /scratch/stefan/7775247/working/building/REAL300004919309 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 309) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/309 `/scratch/stefan/7775247/working/3D/309' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(OC)=CC([N+](=O)[O-])=C1)C(=O)[O-]) `REAL300004919309.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919309 none CC#CCC(NC(=O)C1=CC(OC)=CC([N+](=O)[O-])=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 12, 5, 1, 1, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 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: [97, 97, 97, 30, 7, 7, 1, 7, 1, 1, 1, 1, 2, 1, 1, 1, 2, 2, 1, 30, 47, 47, 97, 97, 97, 97, 97, 30, 7, 1, 3, 3, 3, 1, 1] 152 rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 13, 14, 15, 18, 29] set([0, 1, 2, 3, 4, 5, 7, 12, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 440 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919309 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919309 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919309/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919309 Building REAL300004919310 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919310' /scratch/stefan/7775247/working/building/REAL300004919310 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919310 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919310/0 /scratch/stefan/7775247/working/building/REAL300004919310 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/310 `/scratch/stefan/7775247/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(NC(=O)OC(C)(C)C)C=C1Cl)C(=O)[O-]) `REAL300004919310.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919310 none CC#CCC(NC(=O)C1=CC=C(NC(=O)OC(C)(C)C)C=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 14, 7, 7, 1, 7, 1, 1, 1, 1, 1, 9, 15, 15, 18, 18, 18, 18, 1, 1, 1, 14, 20, 20, 35, 35, 35, 35, 35, 14, 7, 1, 1, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1] 201 rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 12, 45, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919310 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919310 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919310/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919310 Building REAL300004919311 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919311' /scratch/stefan/7775247/working/building/REAL300004919311 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919311 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919311/0 /scratch/stefan/7775247/working/building/REAL300004919311 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 311) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/311 `/scratch/stefan/7775247/working/3D/311' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(C2=CC=CC(C(F)(F)F)=C2)N=N1)C(=O)[O-]) `REAL300004919311.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919311 none CC#CCC(NC(=O)C1=CN(C2=CC=CC(C(F)(F)F)=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 44, 13, 13, 1, 13, 1, 1, 1, 1, 7, 7, 2, 7, 7, 7, 7, 7, 7, 1, 1, 44, 72, 72, 118, 118, 118, 118, 118, 44, 13, 1, 7, 7, 3, 7] 201 rigid atoms, others: [33, 6, 8, 9, 10, 11, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919311 none CC#CCC(NC(=O)C1=CN(C2=CC=CC(C(F)(F)F)=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 125, 54, 54, 7, 54, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 125, 154, 154, 201, 201, 201, 201, 201, 125, 54, 7, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 923 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919311 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919311 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919311/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919311 Building REAL300004919312 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919312' /scratch/stefan/7775247/working/building/REAL300004919312 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919312 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919312/0 /scratch/stefan/7775247/working/building/REAL300004919312 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/312 `/scratch/stefan/7775247/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC(C)C1=CC=C(CC)C=C1)C(=O)[O-]) `REAL300004919312.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919312 none CC#CCC(NC(=O)CC(C)C1=CC=C(CC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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: [42, 42, 42, 33, 21, 21, 6, 21, 3, 1, 3, 1, 1, 1, 1, 1, 3, 1, 1, 33, 33, 33, 42, 42, 42, 42, 42, 33, 21, 6, 6, 3, 3, 3, 3, 1, 1, 3, 3, 3, 3, 3, 1, 1] 73 rigid atoms, others: [35, 36, 9, 42, 11, 12, 13, 14, 15, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 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: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919312 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919312 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919312/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919312 Building REAL300004919313 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919313' /scratch/stefan/7775247/working/building/REAL300004919313 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919313 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919313/0 /scratch/stefan/7775247/working/building/REAL300004919313 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 313) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/313 `/scratch/stefan/7775247/working/3D/313' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CC)OC1=CC=CC=C1C)C(=O)[O-]) `REAL300004919313.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919313 none CC#CCC(NC(=O)C(CC)OC1=CC=CC=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [177, 177, 177, 93, 56, 56, 14, 56, 7, 14, 23, 1, 1, 1, 1, 1, 1, 1, 1, 93, 136, 136, 177, 177, 177, 177, 177, 93, 56, 14, 25, 25, 25, 25, 25, 1, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41]) total number of confs: 1014 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919313 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919313 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919313/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919313 Building REAL300004919314 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919314' /scratch/stefan/7775247/working/building/REAL300004919314 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919314 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919314/0 /scratch/stefan/7775247/working/building/REAL300004919314 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/314 `/scratch/stefan/7775247/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(F)C(CSC)=C1)C(=O)[O-]) `REAL300004919314.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919314 none CC#CCC(NC(=O)C1=CC=C(F)C(CSC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'S.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 5, 14, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 4, 13, 1, 16, 24, 24, 45, 45, 45, 45, 45, 16, 5, 1, 1, 4, 4, 13, 13, 13, 1] 201 rigid atoms, others: [35, 6, 8, 9, 10, 11, 12, 13, 14, 17, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919314 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919314 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919314/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919314 Building REAL300004919315 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919315' /scratch/stefan/7775247/working/building/REAL300004919315 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919315 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919315/0 /scratch/stefan/7775247/working/building/REAL300004919315 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/315 `/scratch/stefan/7775247/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC(C)(C)NC(=O)OC(C)(C)C)C(=O)[O-]) `REAL300004919315.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.0.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.0.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.0.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919315 none CC#CCC(NC(=O)CC(C)(C)NC(=O)OC(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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: [16, 16, 16, 12, 8, 8, 5, 8, 1, 1, 1, 1, 1, 3, 5, 5, 6, 6, 6, 6, 12, 15, 15, 16, 16, 16, 16, 16, 12, 8, 5, 5, 2, 2, 2, 2, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 31 rigid atoms, others: [8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 128 number of broken/clashed sets: 0 ./output.0.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919315 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919315 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919315/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919315 Building REAL300004919316 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919316' /scratch/stefan/7775247/working/building/REAL300004919316 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919316 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919316/0 /scratch/stefan/7775247/working/building/REAL300004919316 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/316 `/scratch/stefan/7775247/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1CN(C(=O)OC(C)(C)C)C1)C(=O)[O-]) `REAL300004919316.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919316 none CC#CCC(NC(=O)CC1CN(C(=O)OC(C)(C)C)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 60, 34, 34, 5, 34, 1, 1, 1, 1, 1, 2, 2, 6, 7, 7, 7, 1, 60, 95, 95, 112, 112, 112, 112, 112, 60, 34, 5, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 45, 44, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 646 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919316 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919316 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919316/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919316 Building REAL300004919317 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919317' /scratch/stefan/7775247/working/building/REAL300004919317 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919317 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919317/0 /scratch/stefan/7775247/working/building/REAL300004919317 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 317) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/317 `/scratch/stefan/7775247/working/3D/317' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(F)C=C1C1=CC=C(Cl)C(Cl)=C1)C(=O)[O-]) `REAL300004919317.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919317 none CC#CCC(NC(=O)C1=CC=C(F)C=C1C1=CC=C(Cl)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 31, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 2, 6, 7, 7, 7, 31, 58, 58, 86, 86, 86, 86, 86, 31, 9, 1, 1, 1, 7, 7, 7] 201 rigid atoms, others: [33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 470 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919317 none CC#CCC(NC(=O)C1=CC=C(F)C=C1C1=CC=C(Cl)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 111, 40, 40, 7, 40, 7, 7, 6, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 111, 143, 143, 201, 201, 201, 201, 201, 111, 40, 7, 6, 7, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 964 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919317 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919317 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919317/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919317 Building REAL300004919318 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919318' /scratch/stefan/7775247/working/building/REAL300004919318 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919318 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919318/0 /scratch/stefan/7775247/working/building/REAL300004919318 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/318 `/scratch/stefan/7775247/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(CC)N(C2=CC=C(OC(C)C)C=C2)N=N1)C(=O)[O-]) `REAL300004919318.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919318 none CC#CCC(NC(=O)C1=C(CC)N(C2=CC=C(OC(C)C)C=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 5, 8, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 6, 1, 1, 1, 3, 1, 1, 4, 4, 2, 2, 17, 44, 42, 4, 4, 1, 1, 18, 29, 29, 45, 45, 45, 45, 45, 18, 6, 3, 3, 3, 3, 3, 4, 4, 42, 44, 43, 44, 43, 43, 42, 4, 4] 201 rigid atoms, others: [6, 8, 9, 10, 12, 13, 23, 24] set([0, 1, 2, 3, 4, 5, 7, 11, 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, 45, 46, 47, 48, 49, 50]) total number of confs: 376 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: REAL300004919318 none CC#CCC(NC(=O)C1=C(CC)N(C2=CC=C(OC(C)C)C=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 5, 8, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 15, 15, 4, 15, 4, 4, 4, 7, 1, 1, 1, 1, 1, 1, 11, 23, 23, 1, 1, 4, 4, 35, 55, 55, 79, 79, 79, 79, 79, 35, 15, 7, 7, 7, 7, 7, 1, 1, 23, 23, 23, 23, 23, 23, 23, 1, 1] 201 rigid atoms, others: [49, 40, 41, 12, 13, 14, 15, 16, 17, 50, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 475 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919318 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919318 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919318/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919318 Building REAL300004919319 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919319' /scratch/stefan/7775247/working/building/REAL300004919319 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919319 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919319/0 /scratch/stefan/7775247/working/building/REAL300004919319 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/319 `/scratch/stefan/7775247/working/3D/319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(CC2=CC=CC(Cl)=C2)CCCC1)C(=O)[O-]) `REAL300004919319.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919319 none CC#CCC(NC(=O)C1(CC2=CC=CC(Cl)=C2)CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [48, 48, 48, 15, 5, 5, 1, 5, 1, 1, 8, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 15, 25, 25, 48, 48, 48, 48, 48, 15, 5, 8, 8, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1] 108 rigid atoms, others: [37, 6, 39, 8, 9, 42, 43, 44, 17, 18, 19, 20, 41, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 259 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: REAL300004919319 none CC#CCC(NC(=O)C1(CC2=CC=CC(Cl)=C2)CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [108, 108, 108, 55, 20, 20, 13, 20, 3, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 55, 78, 78, 108, 108, 108, 108, 108, 55, 20, 3, 3, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13] 108 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16] 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, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 559 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919319 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919319 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919319/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919319 Building REAL300004919320 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919320' /scratch/stefan/7775247/working/building/REAL300004919320 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919320 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919320/0 /scratch/stefan/7775247/working/building/REAL300004919320 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/320 `/scratch/stefan/7775247/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(CSC2=CC(C)=CC=C2C)=C1)C(=O)[O-]) `REAL300004919320.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919320 none CC#CCC(NC(=O)C1=CC=CC(CSC2=CC(C)=CC=C2C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 5, 14, 1, 1, 1, 5, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 3, 15, 33, 33, 33, 27, 33, 33, 33, 1, 12, 17, 17, 31, 31, 31, 31, 31, 12, 5, 1, 1, 1, 3, 3, 33, 33, 33, 33, 27, 33, 33, 33, 33, 1] 201 rigid atoms, others: [34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 48, 23] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919320 none CC#CCC(NC(=O)C1=CC=CC(CSC2=CC(C)=CC=C2C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 5, 14, 1, 1, 1, 5, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 121, 86, 86, 33, 86, 33, 33, 33, 33, 22, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 121, 146, 146, 201, 201, 201, 201, 201, 121, 86, 33, 33, 33, 22, 22, 1, 2, 2, 2, 1, 1, 2, 2, 2, 33] 201 rigid atoms, others: [39, 43, 44, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 45, 46, 47, 48]) total number of confs: 971 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919320 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919320 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919320/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919320 Building REAL300004919321 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919321' /scratch/stefan/7775247/working/building/REAL300004919321 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919321 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919321/0 /scratch/stefan/7775247/working/building/REAL300004919321 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/321 `/scratch/stefan/7775247/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC2=CC=CC(Cl)=C2Cl)C=C1)C(=O)[O-]) `REAL300004919321.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919321 none CC#CCC(NC(=O)C1=CC=C(OC2=CC=CC(Cl)=C2Cl)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 1, 1, 9, 15, 15, 31, 31, 31, 31, 31, 9, 3, 1, 1, 20, 20, 20, 1, 1] 201 rigid atoms, others: [33, 34, 38, 6, 39, 8, 9, 10, 11, 12, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919321 none CC#CCC(NC(=O)C1=CC=C(OC2=CC=CC(Cl)=C2Cl)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 99, 36, 36, 7, 36, 7, 20, 20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 99, 131, 131, 201, 201, 201, 201, 201, 99, 36, 20, 20, 1, 1, 1, 20, 20] 201 rigid atoms, others: [35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39]) total number of confs: 986 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919321 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919321 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919321/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919321 Building REAL300004919322 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919322' /scratch/stefan/7775247/working/building/REAL300004919322 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919322 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919322/0 /scratch/stefan/7775247/working/building/REAL300004919322 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/322 `/scratch/stefan/7775247/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=C(OC)C=CC=C1OC)C(=O)[O-]) `REAL300004919322.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919322 none CC#CCC(NC(=O)CC1=C(OC)C=CC=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 1, 1, 12, 5, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [149, 149, 149, 65, 30, 30, 6, 30, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 3, 65, 101, 101, 149, 149, 149, 149, 149, 65, 30, 6, 6, 4, 4, 4, 1, 1, 1, 3, 3, 3] 201 rigid atoms, others: [34, 35, 36, 8, 9, 10, 11, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39]) total number of confs: 781 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919322 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919322 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919322/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919322 Building REAL300004919323 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919323' /scratch/stefan/7775247/working/building/REAL300004919323 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919323 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919323/0 /scratch/stefan/7775247/working/building/REAL300004919323 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 323) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/323 `/scratch/stefan/7775247/working/3D/323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2F)C(CCC)=N1)C(=O)[O-]) `REAL300004919323.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919323 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2F)C(CCC)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 21, 6, 6, 1, 6, 1, 1, 1, 1, 6, 6, 2, 6, 6, 6, 1, 1, 6, 10, 1, 21, 34, 34, 58, 58, 58, 58, 58, 21, 6, 6, 6, 5, 6, 6, 6, 10, 10, 10, 10, 10] 201 rigid atoms, others: [6, 8, 9, 10, 11, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 339 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919323 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2F)C(CCC)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 127, 47, 19, 19, 6, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 24, 6, 47, 76, 76, 127, 127, 127, 127, 127, 47, 19, 1, 1, 1, 1, 16, 16, 24, 24, 24, 24, 24] 201 rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 712 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919323 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919323 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919323/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919323 Building REAL300004919324 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919324' /scratch/stefan/7775247/working/building/REAL300004919324 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919324 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919324/0 /scratch/stefan/7775247/working/building/REAL300004919324 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/324 `/scratch/stefan/7775247/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2F)C(C(C)C)=N1)C(=O)[O-]) `REAL300004919324.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919324 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2F)C(C(C)C)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 27, 10, 10, 1, 10, 1, 1, 1, 1, 7, 7, 2, 7, 7, 7, 1, 1, 6, 6, 1, 27, 42, 42, 75, 75, 75, 75, 75, 27, 10, 7, 7, 6, 7, 6, 6, 6, 6, 6, 6, 6] 201 rigid atoms, others: [6, 8, 9, 10, 11, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 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: REAL300004919324 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2F)C(C(C)C)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [196, 196, 196, 83, 34, 34, 7, 34, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 7, 83, 124, 124, 196, 196, 196, 196, 196, 83, 34, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15] 201 rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 981 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919324 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919324 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919324/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919324 Building REAL300004919325 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919325' /scratch/stefan/7775247/working/building/REAL300004919325 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919325 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919325/0 /scratch/stefan/7775247/working/building/REAL300004919325 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 325) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/325 `/scratch/stefan/7775247/working/3D/325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1SC1=CC=CC=C1)C(=O)[O-]) `REAL300004919325.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919325 none CC#CCC(NC(=O)C1=CC=CC=C1SC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 27, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 9, 22, 22, 11, 22, 22, 27, 40, 40, 67, 67, 67, 67, 67, 27, 10, 1, 1, 1, 1, 22, 22, 12, 22, 22] 201 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919325 none CC#CCC(NC(=O)C1=CC=CC=C1SC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 117, 72, 76, 22, 76, 22, 22, 19, 22, 22, 6, 1, 1, 1, 1, 1, 1, 1, 117, 147, 147, 201, 201, 201, 201, 201, 117, 76, 22, 22, 22, 22, 1, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 920 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919325 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919325 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919325/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919325 Building REAL300004919326 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919326' /scratch/stefan/7775247/working/building/REAL300004919326 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919326 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919326/0 /scratch/stefan/7775247/working/building/REAL300004919326 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/326 `/scratch/stefan/7775247/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2CCCC2)C2=CC=C(OC)C=C21)C(=O)[O-]) `REAL300004919326.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919326 none CC#CCC(NC(=O)C1=C(C)N(C2CCCC2)C2=CC=C(OC)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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: [103, 103, 103, 35, 11, 11, 1, 11, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 1, 1, 35, 56, 56, 103, 103, 103, 103, 103, 35, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 3, 3, 3, 1] 118 rigid atoms, others: [6, 8, 9, 10, 11, 12, 47, 48, 17, 18, 19, 20, 21, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51]) total number of confs: 506 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: REAL300004919326 none CC#CCC(NC(=O)C1=C(C)N(C2CCCC2)C2=CC=C(OC)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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: [103, 103, 103, 35, 12, 12, 2, 12, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 2, 2, 35, 56, 56, 103, 103, 103, 103, 103, 35, 12, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 2] 118 rigid atoms, others: [45, 43, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 489 number of broken/clashed sets: 117 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919326 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919326 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919326/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919326 Building REAL300004919327 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919327' /scratch/stefan/7775247/working/building/REAL300004919327 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919327 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919327/0 /scratch/stefan/7775247/working/building/REAL300004919327 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 327) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/327 `/scratch/stefan/7775247/working/3D/327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC(Br)=C2OCCOC2=C1)C(=O)[O-]) `REAL300004919327.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919327 none CC#CCC(NC(=O)C=CC1=CC(Br)=C2OCCOC2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 17, 1, 12, 5, 5, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 42, 42, 5, 42, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 119, 147, 147, 201, 201, 201, 201, 201, 119, 42, 5, 5, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 900 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919327 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919327 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919327/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919327 Building REAL300004919328 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919328' /scratch/stefan/7775247/working/building/REAL300004919328 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919328 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919328/0 /scratch/stefan/7775247/working/building/REAL300004919328 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/328 `/scratch/stefan/7775247/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(CNC(=O)OC(C)(C)C)O1)C(=O)[O-]) `REAL300004919328.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919328 none CC#CCC(NC(=O)C1=CC=C(CNC(=O)OC(C)(C)C)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 4, 5, 1, 5, 1, 1, 1, 1, 1, 5, 30, 50, 50, 59, 59, 59, 59, 1, 9, 12, 12, 19, 19, 19, 19, 19, 9, 5, 1, 1, 5, 5, 30, 60, 60, 60, 60, 60, 60, 60, 60, 60] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 283 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919328 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919328 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919328/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919328 Building REAL300004919329 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919329' /scratch/stefan/7775247/working/building/REAL300004919329 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919329 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919329/0 /scratch/stefan/7775247/working/building/REAL300004919329 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 329) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/329 `/scratch/stefan/7775247/working/3D/329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CC)OC1CCCC(C)C1)C(=O)[O-]) `REAL300004919329.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919329 none CC#CCC(NC(=O)C(CC)OC1CCCC(C)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 165, 165, 75, 40, 40, 11, 40, 5, 11, 20, 1, 1, 1, 1, 1, 1, 1, 1, 75, 109, 109, 165, 165, 165, 165, 165, 75, 40, 11, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45]) total number of confs: 891 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919329 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919329 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919329/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919329 Building REAL300004919330 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919330' /scratch/stefan/7775247/working/building/REAL300004919330 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919330 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919330/0 /scratch/stefan/7775247/working/building/REAL300004919330 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/330 `/scratch/stefan/7775247/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CC(F)=C(F)C(F)=C2)C=C1)C(=O)[O-]) `REAL300004919330.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919330 none CC#CCC(NC(=O)C1=CC=C(C2=CC(F)=C(F)C(F)=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 15, 1, 15, 1, 15, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 3, 1, 1, 16, 23, 23, 39, 39, 39, 39, 39, 16, 4, 1, 1, 3, 3, 1, 1] 57 rigid atoms, others: [33, 34, 37, 6, 8, 9, 10, 11, 12, 21, 22, 38] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36]) total number of confs: 188 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919330 none CC#CCC(NC(=O)C1=CC=C(C2=CC(F)=C(F)C(F)=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 15, 1, 15, 1, 15, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 29, 11, 11, 5, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 29, 39, 39, 57, 57, 57, 57, 57, 29, 11, 5, 5, 1, 1, 5, 5] 57 rigid atoms, others: [35, 36, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 273 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919330 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919330 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919330/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919330 Building REAL300004919331 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919331' /scratch/stefan/7775247/working/building/REAL300004919331 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919331 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919331/0 /scratch/stefan/7775247/working/building/REAL300004919331 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/331 `/scratch/stefan/7775247/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(C2=CC=C(Cl)C=C2)N=C1C)C(=O)[O-]) `REAL300004919331.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919331 none CC#CCC(NC(=O)C1=CN(C2=CC=C(Cl)C=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [90, 90, 90, 40, 13, 13, 1, 13, 1, 1, 1, 1, 4, 4, 1, 2, 4, 4, 1, 1, 1, 40, 58, 58, 90, 90, 90, 90, 90, 40, 13, 1, 4, 4, 4, 4, 2, 2, 2] 91 rigid atoms, others: [6, 8, 9, 10, 11, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 443 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919331 none CC#CCC(NC(=O)C1=CN(C2=CC=C(Cl)C=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 51, 25, 25, 4, 25, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 51, 68, 68, 91, 91, 91, 91, 91, 51, 25, 4, 1, 1, 1, 1, 4, 4, 4] 91 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 421 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919331 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919331 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919331/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919331 Building REAL300004919332 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919332' /scratch/stefan/7775247/working/building/REAL300004919332 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919332 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919332/0 /scratch/stefan/7775247/working/building/REAL300004919332 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/332 `/scratch/stefan/7775247/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=NN(C2=CC=C(F)C=C2)C=C1)C(=O)[O-]) `REAL300004919332.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919332 none CC#CCC(NC(=O)CC1=NN(C2=CC=C(F)C=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 97, 45, 45, 7, 45, 1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 1, 1, 97, 139, 139, 201, 201, 201, 201, 201, 97, 45, 7, 7, 4, 4, 4, 4, 1, 1] 201 rigid atoms, others: [37, 38, 8, 9, 10, 11, 12, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 1023 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919332 none CC#CCC(NC(=O)CC1=NN(C2=CC=C(F)C=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 103, 52, 52, 12, 52, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 103, 146, 146, 201, 201, 201, 201, 201, 103, 52, 12, 12, 1, 1, 1, 1, 4, 3] 201 rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 1013 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919332 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919332 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919332/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919332 Building REAL300004919333 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919333' /scratch/stefan/7775247/working/building/REAL300004919333 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919333 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919333/0 /scratch/stefan/7775247/working/building/REAL300004919333 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/333 `/scratch/stefan/7775247/working/3D/333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC(C)C1=CC=C(OC)C=C1)C(=O)[O-]) `REAL300004919333.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919333 none CC#CCC(NC(=O)CC(C)C1=CC=C(OC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 46, 27, 27, 6, 27, 3, 1, 3, 1, 1, 1, 1, 1, 3, 1, 1, 46, 46, 46, 71, 71, 71, 71, 71, 46, 27, 6, 6, 3, 3, 3, 3, 1, 1, 3, 3, 3, 1, 1] 71 rigid atoms, others: [35, 36, 40, 9, 11, 12, 13, 14, 15, 17, 18, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39]) total number of confs: 317 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919333 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919333 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919333/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919333 Building REAL300004919334 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919334' /scratch/stefan/7775247/working/building/REAL300004919334 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919334 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919334/0 /scratch/stefan/7775247/working/building/REAL300004919334 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/334 `/scratch/stefan/7775247/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)CC1=CC=C(OC)C=C1)C(=O)[O-]) `REAL300004919334.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919334 none CC#CCC(NC(=O)C(C)CC1=CC=C(OC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [161, 161, 161, 79, 26, 26, 5, 26, 2, 5, 1, 1, 1, 1, 1, 1, 2, 1, 1, 79, 124, 124, 161, 161, 161, 161, 161, 79, 26, 5, 5, 5, 5, 2, 2, 1, 1, 3, 3, 3, 1, 1] 198 rigid atoms, others: [35, 36, 40, 41, 10, 11, 12, 13, 14, 15, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39]) total number of confs: 869 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919334 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919334 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919334/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919334 Building REAL300004919335 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919335' /scratch/stefan/7775247/working/building/REAL300004919335 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919335 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919335/0 /scratch/stefan/7775247/working/building/REAL300004919335 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 335) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/335 `/scratch/stefan/7775247/working/3D/335' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)(C)C1=CC=C(OC)C=C1)C(=O)[O-]) `REAL300004919335.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919335 none CC#CCC(NC(=O)C(C)(C)C1=CC=C(OC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [151, 151, 151, 65, 27, 27, 7, 27, 1, 7, 7, 1, 1, 1, 1, 1, 2, 1, 1, 65, 106, 106, 151, 151, 151, 151, 151, 65, 27, 7, 7, 7, 7, 7, 7, 1, 1, 3, 3, 3, 1, 1] 201 rigid atoms, others: [35, 36, 8, 41, 11, 12, 13, 14, 15, 17, 18, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39]) total number of confs: 792 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919335 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919335 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919335/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919335 Building REAL300004919336 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919336' /scratch/stefan/7775247/working/building/REAL300004919336 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919336 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919336/0 /scratch/stefan/7775247/working/building/REAL300004919336 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/336 `/scratch/stefan/7775247/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC(C)(C)C)C=C1)C(=O)[O-]) `REAL300004919336.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919336 none CC#CCC(NC(=O)C1=CC=C(OC(C)(C)C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [41, 41, 41, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 3, 7, 7, 7, 1, 1, 16, 24, 24, 41, 41, 41, 41, 41, 16, 4, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1] 108 rigid atoms, others: [6, 8, 9, 10, 11, 12, 17, 18, 41, 40, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 206 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919336 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919336 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919336/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919336 Building REAL300004919337 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919337' /scratch/stefan/7775247/working/building/REAL300004919337 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919337 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919337/0 /scratch/stefan/7775247/working/building/REAL300004919337 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 337) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/337 `/scratch/stefan/7775247/working/3D/337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC(C)C1=CC=CC(OC)=C1)C(=O)[O-]) `REAL300004919337.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919337 none CC#CCC(NC(=O)CC(C)C1=CC=CC(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 78, 46, 46, 12, 46, 4, 1, 4, 1, 1, 1, 1, 1, 1, 2, 1, 78, 78, 78, 118, 118, 118, 118, 118, 78, 46, 12, 12, 4, 5, 5, 5, 1, 1, 1, 3, 3, 3, 1] 130 rigid atoms, others: [35, 36, 37, 9, 11, 12, 13, 14, 15, 16, 18, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40]) total number of confs: 531 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919337 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919337 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919337/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919337 Building REAL300004919338 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919338' /scratch/stefan/7775247/working/building/REAL300004919338 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919338 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919338/0 /scratch/stefan/7775247/working/building/REAL300004919338 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/338 `/scratch/stefan/7775247/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CC)OC1=CC=CC(C)=C1)C(=O)[O-]) `REAL300004919338.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919338 none CC#CCC(NC(=O)C(CC)OC1=CC=CC(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 165, 165, 87, 59, 59, 20, 59, 10, 20, 36, 1, 1, 1, 1, 1, 1, 1, 1, 87, 129, 129, 165, 165, 165, 165, 165, 87, 59, 20, 39, 39, 39, 39, 39, 1, 1, 1, 2, 2, 2, 1] 201 rigid atoms, others: [35, 36, 37, 41, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40]) total number of confs: 1000 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919338 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919338 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919338/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919338 Building REAL300004919339 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919339' /scratch/stefan/7775247/working/building/REAL300004919339 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919339 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919339/0 /scratch/stefan/7775247/working/building/REAL300004919339 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/339 `/scratch/stefan/7775247/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC=C(S(C)(=O)=O)C=C1)C(=O)[O-]) `REAL300004919339.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919339 none CC#CCC(NC(=O)COC1=CC=C(S(C)(=O)=O)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 139, 107, 65, 65, 13, 65, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 107, 115, 115, 139, 139, 139, 139, 139, 107, 65, 13, 13, 1, 1, 3, 3, 3, 1, 1] 201 rigid atoms, others: [32, 33, 37, 38, 9, 10, 11, 12, 13, 14, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 620 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919339 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919339 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919339/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919339 Building REAL300004919340 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919340' /scratch/stefan/7775247/working/building/REAL300004919340 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919340 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919340/0 /scratch/stefan/7775247/working/building/REAL300004919340 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/340 `/scratch/stefan/7775247/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(S(=O)(=O)N(C)C)=CN1)C(=O)[O-]) `REAL300004919340.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919340 none CC#CCC(NC(=O)C1=CC(S(=O)(=O)N(C)C)=CN1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 24, 9, 9, 1, 9, 1, 1, 1, 1, 8, 8, 8, 19, 19, 1, 1, 24, 38, 38, 63, 63, 63, 63, 63, 24, 9, 1, 20, 20, 20, 20, 20, 20, 1, 1] 201 rigid atoms, others: [36, 37, 6, 8, 9, 10, 11, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 380 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919340 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919340 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919340/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919340 Building REAL300004919341 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919341' /scratch/stefan/7775247/working/building/REAL300004919341 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919341 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919341/0 /scratch/stefan/7775247/working/building/REAL300004919341 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 341) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/341 `/scratch/stefan/7775247/working/3D/341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(N2C=C(Br)C=N2)C=C1)C(=O)[O-]) `REAL300004919341.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919341 none CC#CCC(NC(=O)C1=CC=C(N2C=C(Br)C=N2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'Br', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 17, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 13, 20, 20, 38, 38, 38, 38, 38, 13, 4, 1, 1, 6, 6, 1, 1] 66 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919341 none CC#CCC(NC(=O)C1=CC=C(N2C=C(Br)C=N2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'Br', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 17, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 31, 11, 11, 2, 11, 2, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 31, 39, 39, 66, 66, 66, 66, 66, 31, 11, 6, 6, 1, 1, 6, 6] 66 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 309 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919341 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919341 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919341/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919341 Building REAL300004919342 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919342' /scratch/stefan/7775247/working/building/REAL300004919342 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919342 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919342/0 /scratch/stefan/7775247/working/building/REAL300004919342 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/342 `/scratch/stefan/7775247/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Cl)=CC=C1N1C=NN=N1)C(=O)[O-]) `REAL300004919342.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919342 none CC#CCC(NC(=O)C1=CC(Cl)=CC=C1N1C=NN=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 1, 1, 8, 1, 8, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 24, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 24, 35, 35, 66, 66, 66, 66, 66, 24, 9, 1, 1, 1, 9] 95 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 315 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919342 none CC#CCC(NC(=O)C1=CC(Cl)=CC=C1N1C=NN=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 1, 1, 8, 1, 8, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 43, 22, 22, 9, 22, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 43, 60, 60, 95, 95, 95, 95, 95, 43, 22, 9, 9, 9, 1] 95 rigid atoms, others: [33, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 446 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919342 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919342 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919342/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919342 Building REAL300004919343 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919343' /scratch/stefan/7775247/working/building/REAL300004919343 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919343 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919343/0 /scratch/stefan/7775247/working/building/REAL300004919343 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/343 `/scratch/stefan/7775247/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)OC1=CC=C2CCCC2=C1)C(=O)[O-]) `REAL300004919343.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919343 none CC#CCC(NC(=O)C(C)OC1=CC=C2CCCC2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 159, 102, 102, 25, 102, 11, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 159, 172, 172, 201, 201, 201, 201, 201, 159, 102, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 865 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919343 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919343 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919343/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919343 Building REAL300004919344 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919344' /scratch/stefan/7775247/working/building/REAL300004919344 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919344 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919344/0 /scratch/stefan/7775247/working/building/REAL300004919344 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/344 `/scratch/stefan/7775247/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C2NC3=C(CCCCC3)C2=C1)C(=O)[O-]) `REAL300004919344.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919344 none CC#CCC(NC(=O)C1=CC=C2NC3=C(CCCCC3)C2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 36, 36, 67, 67, 67, 67, 67, 26, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 67 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 5, 7, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 301 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919344 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919344 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919344/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919344 Building REAL300004919345 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919345' /scratch/stefan/7775247/working/building/REAL300004919345 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919345 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919345/0 /scratch/stefan/7775247/working/building/REAL300004919345 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/345 `/scratch/stefan/7775247/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=C(Cl)C(Cl)=CC=C2N1)C(=O)[O-]) `REAL300004919345.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919345 none CC#CCC(NC(=O)C1=CC2=C(Cl)C(Cl)=CC=C2N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 16, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 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: [74, 74, 74, 38, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 53, 53, 74, 74, 74, 74, 74, 38, 12, 1, 1, 1, 1] 74 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 358 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919345 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919345 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919345/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919345 Building REAL300004919346 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919346' /scratch/stefan/7775247/working/building/REAL300004919346 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919346 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919346/0 /scratch/stefan/7775247/working/building/REAL300004919346 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/346 `/scratch/stefan/7775247/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=C(Br)C=C2)CCCCC1)C(=O)[O-]) `REAL300004919346.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919346 none CC#CCC(NC(=O)C1(C2=CC=C(Br)C=C2)CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 20, 5, 5, 1, 5, 1, 1, 7, 7, 1, 7, 7, 7, 1, 1, 1, 1, 1, 20, 34, 34, 72, 72, 72, 72, 72, 20, 5, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 97 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 42, 43, 44, 16, 17, 18, 19, 20, 41, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 347 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919346 none CC#CCC(NC(=O)C1(C2=CC=C(Br)C=C2)CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 17, 1, 1, 5, 5, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 97, 47, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 47, 66, 66, 97, 97, 97, 97, 97, 47, 18, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 97 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 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]) total number of confs: 470 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919346 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919346 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919346/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919346 Building REAL300004919347 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919347' /scratch/stefan/7775247/working/building/REAL300004919347 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919347 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919347/0 /scratch/stefan/7775247/working/building/REAL300004919347 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 347) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/347 `/scratch/stefan/7775247/working/3D/347' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=C(OCC2=C(C)ON=C2C)C=C1)C(=O)[O-]) `REAL300004919347.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919347 none CC#CCC(NC(=O)CC1=CC=C(OCC2=C(C)ON=C2C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 12, 5, 1, 1, 5, 12, 8, 1, 5, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 9, 9, 3, 9, 1, 1, 1, 1, 1, 1, 2, 2, 14, 14, 14, 14, 14, 14, 1, 1, 16, 19, 19, 27, 27, 27, 27, 27, 16, 9, 3, 3, 1, 1, 2, 2, 14, 14, 14, 14, 14, 14, 1, 1] 201 rigid atoms, others: [36, 37, 8, 9, 10, 11, 12, 13, 46, 47, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919347 none CC#CCC(NC(=O)CC1=CC=C(OCC2=C(C)ON=C2C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 12, 5, 1, 1, 5, 12, 8, 1, 5, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 108, 65, 65, 24, 65, 14, 14, 14, 14, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 108, 140, 140, 201, 201, 201, 201, 201, 108, 65, 24, 24, 14, 14, 8, 8, 2, 2, 2, 2, 2, 2, 14, 14] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 1033 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919347 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919347 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919347/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919347 Building REAL300004919348 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919348' /scratch/stefan/7775247/working/building/REAL300004919348 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919348 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919348/0 /scratch/stefan/7775247/working/building/REAL300004919348 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/348 `/scratch/stefan/7775247/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(SCCC(C)C)C([N+](=O)[O-])=C1)C(=O)[O-]) `REAL300004919348.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919348 none CC#CCC(NC(=O)C1=CC=C(SCCC(C)C)C([N+](=O)[O-])=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 14, 5, 5, 5, 5, 5, 1, 8, 11, 11, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 5, 5, 1, 5, 1, 1, 1, 1, 1, 8, 21, 24, 24, 24, 1, 1, 2, 2, 1, 12, 20, 20, 34, 34, 34, 34, 34, 12, 5, 1, 1, 21, 21, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1] 201 rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 12, 46, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919348 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919348 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919348/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919348 Building REAL300004919349 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919349' /scratch/stefan/7775247/working/building/REAL300004919349 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919349 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919349/0 /scratch/stefan/7775247/working/building/REAL300004919349 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/349 `/scratch/stefan/7775247/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(NC)C([N+](=O)[O-])=C1)C(=O)[O-]) `REAL300004919349.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919349 none CC#CCC(NC(=O)C1=CC=C(NC)C([N+](=O)[O-])=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 6, 1, 1, 2, 2, 1, 26, 42, 42, 78, 78, 78, 78, 78, 26, 7, 1, 1, 6, 6, 6, 6, 1] 79 rigid atoms, others: [35, 6, 8, 9, 10, 11, 12, 14, 15, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 380 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919349 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919349 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919349/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919349 Building REAL300004919350 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919350' /scratch/stefan/7775247/working/building/REAL300004919350 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919350 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919350/0 /scratch/stefan/7775247/working/building/REAL300004919350 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/350 `/scratch/stefan/7775247/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=C(NC(=O)OC(C)(C)C)C=C1)C(=O)[O-]) `REAL300004919350.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919350 none CC#CCC(NC(=O)CC1=CC=C(NC(=O)OC(C)(C)C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 9, 9, 4, 9, 1, 1, 1, 1, 1, 1, 9, 13, 13, 14, 14, 14, 14, 1, 1, 19, 23, 23, 37, 37, 37, 37, 37, 19, 9, 4, 4, 1, 1, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1] 201 rigid atoms, others: [35, 36, 8, 9, 10, 11, 12, 13, 47, 48, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919350 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919350 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919350/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919350 Building REAL300004919351 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919351' /scratch/stefan/7775247/working/building/REAL300004919351 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919351 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919351/0 /scratch/stefan/7775247/working/building/REAL300004919351 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/351 `/scratch/stefan/7775247/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC(Br)=CS1)C(=O)[O-]) `REAL300004919351.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919351 none CC#CCC(NC(=O)C=CC1=CC(Br)=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 17, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 128, 72, 72, 13, 71, 13, 1, 1, 1, 1, 1, 1, 1, 128, 162, 162, 201, 201, 201, 201, 201, 128, 72, 13, 13, 1, 1] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 911 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919351 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919351 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919351/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919351 Building REAL300004919352 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919352' /scratch/stefan/7775247/working/building/REAL300004919352 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919352 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919352/0 /scratch/stefan/7775247/working/building/REAL300004919352 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/352 `/scratch/stefan/7775247/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)OC(S(=O)(=O)N(C)C)=C1)C(=O)[O-]) `REAL300004919352.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919352 none CC#CCC(NC(=O)C1=C(C)OC(S(=O)(=O)N(C)C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 5, 12, 1, 14, 11, 11, 8, 5, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 3, 7, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 24, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 8, 8, 8, 17, 17, 1, 24, 41, 41, 57, 57, 57, 57, 57, 24, 9, 2, 2, 2, 17, 17, 17, 18, 18, 18, 1] 201 rigid atoms, others: [6, 39, 8, 9, 10, 11, 12, 13, 19] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 368 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919352 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919352 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919352/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919352 Building REAL300004919353 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919353' /scratch/stefan/7775247/working/building/REAL300004919353 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919353 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919353/0 /scratch/stefan/7775247/working/building/REAL300004919353 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/353 `/scratch/stefan/7775247/working/3D/353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(NC(=O)OC(C)(C)C)CC1)C(=O)[O-]) `REAL300004919353.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919353 none CC#CCC(NC(=O)C1(NC(=O)OC(C)(C)C)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 104, 39, 13, 13, 1, 13, 1, 1, 3, 5, 5, 15, 17, 17, 17, 1, 1, 39, 59, 59, 104, 104, 104, 104, 104, 39, 13, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1] 201 rigid atoms, others: [6, 39, 8, 9, 42, 17, 18, 41, 40] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 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: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919353 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919353 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919353/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919353 Building REAL300004919354 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919354' /scratch/stefan/7775247/working/building/REAL300004919354 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919354 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919354/0 /scratch/stefan/7775247/working/building/REAL300004919354 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/354 `/scratch/stefan/7775247/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(Br)C(C)=NN1C)C(=O)[O-]) `REAL300004919354.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919354 none CC#CCC(NC(=O)C1=C(Br)C(C)=NN1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 17, 1, 5, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 23, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 23, 36, 36, 70, 70, 70, 70, 70, 23, 6, 2, 2, 2, 2, 2, 2] 70 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 332 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919354 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919354 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919354/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919354 Building REAL300004919355 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919355' /scratch/stefan/7775247/working/building/REAL300004919355 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919355 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919355/0 /scratch/stefan/7775247/working/building/REAL300004919355 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 355) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/355 `/scratch/stefan/7775247/working/3D/355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1CCN(C(=O)OC(C)(C)C)CC1)C(=O)[O-]) `REAL300004919355.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919355 none CC#CCC(NC(=O)CC1CCN(C(=O)OC(C)(C)C)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 51, 23, 23, 10, 23, 1, 1, 1, 1, 1, 1, 4, 4, 11, 12, 12, 12, 1, 1, 51, 79, 79, 100, 100, 100, 100, 100, 51, 23, 10, 10, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 48, 49, 50, 51, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 576 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919355 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919355 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919355/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919355 Building REAL300004919356 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919356' /scratch/stefan/7775247/working/building/REAL300004919356 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919356 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919356/0 /scratch/stefan/7775247/working/building/REAL300004919356 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/356 `/scratch/stefan/7775247/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN=C(C2=CC=CC=C2)N=C1C)C(=O)[O-]) `REAL300004919356.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919356 none CC#CCC(NC(=O)C1=CN=C(C2=CC=CC=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [123, 123, 123, 44, 10, 10, 1, 10, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 1, 1, 44, 67, 67, 123, 123, 123, 123, 123, 44, 10, 1, 6, 6, 1, 6, 6, 2, 2, 2] 157 rigid atoms, others: [6, 8, 9, 10, 11, 12, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 576 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919356 none CC#CCC(NC(=O)C1=CN=C(C2=CC=CC=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 124, 53, 13, 13, 1, 13, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 53, 78, 78, 125, 125, 126, 125, 126, 53, 13, 6, 1, 1, 1, 1, 1, 7, 7, 7] 157 rigid atoms, others: [32, 33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39]) total number of confs: 611 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919356 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919356 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919356/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919356 Building REAL300004919357 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919357' /scratch/stefan/7775247/working/building/REAL300004919357 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919357 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919357/0 /scratch/stefan/7775247/working/building/REAL300004919357 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/357 `/scratch/stefan/7775247/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Br)=C(Br)N1C)C(=O)[O-]) `REAL300004919357.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919357 none CC#CCC(NC(=O)C1=CC(Br)=C(Br)N1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'Br', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 17, 1, 17, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 39, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 39, 54, 54, 73, 73, 73, 73, 73, 39, 13, 1, 2, 2, 2] 73 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 26] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29]) total number of confs: 366 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919357 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919357 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919357/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919357 Building REAL300004919358 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919358' /scratch/stefan/7775247/working/building/REAL300004919358 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919358 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919358/0 /scratch/stefan/7775247/working/building/REAL300004919358 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/358 `/scratch/stefan/7775247/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(N2C=CC(C)=N2)C=C1)C(=O)[O-]) `REAL300004919358.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919358 none CC#CCC(NC(=O)C1=CC=C(N2C=CC(C)=N2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 5, 8, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 13, 20, 20, 39, 39, 39, 39, 39, 13, 4, 1, 1, 7, 7, 7, 7, 7, 1, 1] 68 rigid atoms, others: [37, 6, 8, 9, 10, 11, 12, 18, 19, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919358 none CC#CCC(NC(=O)C1=CC=C(N2C=CC(C)=N2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 5, 8, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 32, 11, 11, 2, 11, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 32, 43, 43, 68, 68, 68, 68, 68, 32, 11, 7, 7, 1, 1, 2, 2, 2, 7, 7] 68 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 339 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919358 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919358 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919358/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919358 Building REAL300004919359 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919359' /scratch/stefan/7775247/working/building/REAL300004919359 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919359 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919359/0 /scratch/stefan/7775247/working/building/REAL300004919359 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/359 `/scratch/stefan/7775247/working/3D/359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C2CC2)N(C2=CC=CC=C2)N=C1)C(=O)[O-]) `REAL300004919359.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919359 none CC#CCC(NC(=O)C1=C(C2CC2)N(C2=CC=CC=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [104, 104, 104, 42, 13, 13, 1, 13, 1, 1, 1, 5, 5, 1, 1, 6, 6, 1, 6, 6, 1, 1, 42, 61, 61, 104, 104, 104, 104, 104, 42, 13, 5, 5, 5, 5, 5, 6, 6, 3, 6, 6, 1] 119 rigid atoms, others: [6, 8, 9, 10, 13, 14, 20, 21, 42] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 513 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919359 none CC#CCC(NC(=O)C1=C(C2CC2)N(C2=CC=CC=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 119, 70, 29, 29, 6, 29, 6, 6, 6, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 70, 88, 88, 119, 119, 119, 119, 119, 70, 29, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 6] 119 rigid atoms, others: [37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42]) 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: REAL300004919359 none CC#CCC(NC(=O)C1=C(C2CC2)N(C2=CC=CC=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 119, 62, 23, 23, 5, 23, 5, 1, 1, 1, 1, 5, 5, 8, 8, 5, 8, 8, 5, 5, 62, 84, 84, 119, 119, 119, 119, 119, 62, 23, 1, 1, 1, 1, 1, 8, 8, 5, 8, 8, 5] 119 rigid atoms, others: [32, 33, 34, 35, 36, 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, 37, 38, 39, 40, 41, 42]) total number of confs: 578 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919359 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919359 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919359/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919359 Building REAL300004919360 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919360' /scratch/stefan/7775247/working/building/REAL300004919360 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919360 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919360/0 /scratch/stefan/7775247/working/building/REAL300004919360 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/360 `/scratch/stefan/7775247/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=CC(OC)=C(OC)C(OC)=C2N1)C(=O)[O-]) `REAL300004919360.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919360 none CC#CCC(NC(=O)C1=CC2=CC(OC)=C(OC)C(OC)=C2N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 12, 5, 1, 8, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 24, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 3, 1, 1, 7, 1, 1, 6, 1, 1, 24, 41, 41, 68, 68, 68, 68, 68, 24, 9, 1, 1, 4, 4, 4, 7, 7, 7, 6, 6, 6, 1] 201 rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 12, 13, 15, 16, 18, 19, 21, 22, 44] set([0, 1, 2, 3, 4, 5, 7, 14, 17, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 358 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919360 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919360 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919360/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919360 Building REAL300004919361 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919361' /scratch/stefan/7775247/working/building/REAL300004919361 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919361 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919361/0 /scratch/stefan/7775247/working/building/REAL300004919361 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 361) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/361 `/scratch/stefan/7775247/working/3D/361' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(C2=CC=C(Cl)C=C2)N=N1)C(=O)[O-]) `REAL300004919361.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919361 none CC#CCC(NC(=O)C1=CN(C2=CC=C(Cl)C=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [68, 68, 68, 36, 13, 13, 1, 13, 1, 1, 1, 1, 4, 4, 1, 1, 4, 4, 1, 1, 36, 51, 51, 68, 68, 68, 68, 68, 36, 13, 1, 4, 4, 4, 4] 75 rigid atoms, others: [6, 8, 9, 10, 11, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919361 none CC#CCC(NC(=O)C1=CN(C2=CC=C(Cl)C=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [75, 75, 75, 46, 20, 20, 4, 20, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 46, 59, 59, 75, 75, 75, 75, 75, 46, 20, 4, 1, 1, 1, 1] 75 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 353 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919361 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919361 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919361/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919361 Building REAL300004919362 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919362' /scratch/stefan/7775247/working/building/REAL300004919362 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919362 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919362/0 /scratch/stefan/7775247/working/building/REAL300004919362 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/362 `/scratch/stefan/7775247/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(C2=CC=CC=C2C(F)(F)F)N=N1)C(=O)[O-]) `REAL300004919362.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919362 none CC#CCC(NC(=O)C1=CN(C2=CC=CC=C2C(F)(F)F)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 46, 13, 13, 1, 13, 1, 1, 1, 1, 7, 7, 1, 7, 7, 7, 7, 7, 7, 1, 1, 46, 66, 66, 118, 118, 118, 118, 118, 46, 13, 1, 7, 7, 3, 7] 201 rigid atoms, others: [33, 6, 8, 9, 10, 11, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37]) total number of confs: 563 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919362 none CC#CCC(NC(=O)C1=CN(C2=CC=CC=C2C(F)(F)F)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 51, 51, 7, 51, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 131, 152, 152, 201, 201, 201, 201, 201, 131, 51, 7, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 894 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919362 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919362 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919362/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919362 Building REAL300004919363 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919363' /scratch/stefan/7775247/working/building/REAL300004919363 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919363 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919363/0 /scratch/stefan/7775247/working/building/REAL300004919363 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 363) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/363 `/scratch/stefan/7775247/working/3D/363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CC=C(Br)C=C2)S1)C(=O)[O-]) `REAL300004919363.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919363 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(Br)C=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 40, 13, 13, 1, 13, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 6, 1, 40, 62, 62, 88, 88, 88, 88, 88, 40, 13, 1, 1, 6, 6, 6, 6] 157 rigid atoms, others: [6, 8, 9, 10, 11, 12, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 467 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919363 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(Br)C=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [157, 157, 157, 109, 61, 61, 6, 61, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 109, 130, 130, 157, 157, 157, 157, 157, 109, 61, 6, 6, 1, 1, 1, 1] 157 rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 687 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919363 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919363 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919363/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919363 Building REAL300004919364 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919364' /scratch/stefan/7775247/working/building/REAL300004919364 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919364 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919364/0 /scratch/stefan/7775247/working/building/REAL300004919364 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/364 `/scratch/stefan/7775247/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=CC(OC)=CC=C2OC1)C(=O)[O-]) `REAL300004919364.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919364 none CC#CCC(NC(=O)C1=CC2=CC(OC)=CC=C2OC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 12, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 119, 48, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 48, 79, 79, 119, 119, 119, 119, 119, 48, 12, 1, 1, 2, 2, 2, 1, 1, 1, 1] 163 rigid atoms, others: [35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 32, 34, 14, 33, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 595 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919364 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919364 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919364/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919364 Building REAL300004919365 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919365' /scratch/stefan/7775247/working/building/REAL300004919365 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919365 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919365/0 /scratch/stefan/7775247/working/building/REAL300004919365 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 365) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/365 `/scratch/stefan/7775247/working/3D/365' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(C2=CC=C(Br)C=C2)N=N1)C(=O)[O-]) `REAL300004919365.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919365 none CC#CCC(NC(=O)C1=CN(C2=CC=C(Br)C=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [70, 70, 70, 38, 13, 13, 1, 13, 1, 1, 1, 1, 4, 4, 2, 2, 4, 4, 1, 1, 38, 53, 53, 70, 70, 70, 70, 70, 38, 13, 1, 4, 4, 4, 4] 77 rigid atoms, others: [6, 8, 9, 10, 11, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 350 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919365 none CC#CCC(NC(=O)C1=CN(C2=CC=C(Br)C=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 17, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 48, 20, 20, 4, 20, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 48, 61, 61, 77, 77, 77, 77, 77, 48, 20, 4, 1, 1, 1, 1] 77 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 362 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919365 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919365 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919365/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919365 Building REAL300004919366 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919366' /scratch/stefan/7775247/working/building/REAL300004919366 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919366 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919366/0 /scratch/stefan/7775247/working/building/REAL300004919366 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/366 `/scratch/stefan/7775247/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)N2CCOCC2)O1)C(=O)[O-]) `REAL300004919366.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919366 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)N2CCOCC2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 12, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 6, 1, 1, 1, 1, 1, 8, 8, 8, 35, 35, 35, 35, 35, 1, 17, 26, 26, 38, 38, 38, 38, 38, 17, 6, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41]) 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: REAL300004919366 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)N2CCOCC2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 12, 5, 5, 12, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 3, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 143, 87, 86, 34, 87, 34, 34, 34, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 34, 143, 167, 167, 201, 201, 201, 201, 201, 143, 86, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 12, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 881 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919366 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919366 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919366/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919366 Building REAL300004919367 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919367' /scratch/stefan/7775247/working/building/REAL300004919367 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919367 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919367/0 /scratch/stefan/7775247/working/building/REAL300004919367 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 367) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/367 `/scratch/stefan/7775247/working/3D/367' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=CC=C(OC)C=C2)N=N1)C(=O)[O-]) `REAL300004919367.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919367 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=C(OC)C=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 12, 5, 1, 1, 8, 8, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 35, 11, 11, 1, 11, 1, 1, 1, 1, 1, 4, 4, 2, 3, 6, 4, 4, 1, 1, 35, 57, 57, 92, 92, 92, 92, 92, 35, 11, 2, 2, 2, 4, 4, 6, 6, 6, 4, 4] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 485 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919367 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=C(OC)C=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 12, 5, 1, 1, 8, 8, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [164, 164, 164, 66, 24, 24, 4, 24, 4, 4, 4, 1, 1, 1, 1, 1, 1, 2, 1, 1, 4, 4, 66, 105, 105, 164, 164, 164, 164, 164, 66, 24, 4, 4, 4, 1, 1, 3, 3, 3, 1, 1] 201 rigid atoms, others: [35, 36, 40, 41, 11, 12, 13, 14, 15, 16, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39]) total number of confs: 837 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919367 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919367 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919367/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919367 Building REAL300004919368 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919368' /scratch/stefan/7775247/working/building/REAL300004919368 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919368 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919368/0 /scratch/stefan/7775247/working/building/REAL300004919368 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/368 `/scratch/stefan/7775247/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(Cl)C2=CC(C)=CC=C2N1)C(=O)[O-]) `REAL300004919368.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919368 none CC#CCC(NC(=O)C1=C(Cl)C2=CC(C)=CC=C2N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 16, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 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: [59, 59, 59, 22, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 33, 33, 59, 59, 59, 59, 59, 22, 6, 1, 2, 2, 2, 1, 1, 1] 59 rigid atoms, others: [33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 7, 32, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 279 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919368 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919368 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919368/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919368 Building REAL300004919369 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919369' /scratch/stefan/7775247/working/building/REAL300004919369 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919369 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919369/0 /scratch/stefan/7775247/working/building/REAL300004919369 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 369) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/369 `/scratch/stefan/7775247/working/3D/369' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Br)=CS1)C(=O)[O-]) `REAL300004919369.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919369 none CC#CCC(NC(=O)C1=CC(Br)=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 17, 1, 14, 1, 11, 11, 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, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 35, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 35, 46, 46, 58, 58, 58, 58, 58, 35, 12, 1, 1] 66 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 270 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919369 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919369 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919369/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919369 Building REAL300004919370 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919370' /scratch/stefan/7775247/working/building/REAL300004919370 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919370 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919370/0 /scratch/stefan/7775247/working/building/REAL300004919370 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/370 `/scratch/stefan/7775247/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(N2C=CN=C2)C([N+](=O)[O-])=C1)C(=O)[O-]) `REAL300004919370.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919370 none CC#CCC(NC(=O)C1=CC=C(N2C=CN=C2)C([N+](=O)[O-])=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 29, 7, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 2, 2, 1, 29, 43, 43, 76, 76, 76, 76, 76, 29, 7, 1, 1, 7, 7, 7, 1] 151 rigid atoms, others: [32, 33, 37, 6, 8, 9, 10, 11, 12, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 358 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919370 none CC#CCC(NC(=O)C1=CC=C(N2C=CN=C2)C([N+](=O)[O-])=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [151, 151, 151, 77, 27, 27, 6, 27, 6, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 77, 99, 99, 151, 151, 151, 151, 151, 77, 27, 7, 7, 1, 1, 1, 7] 151 rigid atoms, others: [34, 35, 36, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37]) total number of confs: 675 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919370 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919370 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919370/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919370 Building REAL300004919371 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919371' /scratch/stefan/7775247/working/building/REAL300004919371 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919371 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919371/0 /scratch/stefan/7775247/working/building/REAL300004919371 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 371) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/371 `/scratch/stefan/7775247/working/3D/371' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC(C)NC(=O)OC(C)(C)C)C(=O)[O-]) `REAL300004919371.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.0.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.0.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.0.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919371 none CC#CCC(NC(=O)CC(C)NC(=O)OC(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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: [18, 18, 18, 9, 6, 6, 3, 6, 1, 1, 1, 1, 4, 6, 6, 6, 6, 6, 6, 9, 14, 14, 18, 18, 18, 18, 18, 9, 6, 3, 3, 1, 2, 2, 2, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 31 rigid atoms, others: [8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 116 number of broken/clashed sets: 0 ./output.0.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919371 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919371 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919371/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919371 Building REAL300004919372 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919372' /scratch/stefan/7775247/working/building/REAL300004919372 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919372 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919372/0 /scratch/stefan/7775247/working/building/REAL300004919372 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/372 `/scratch/stefan/7775247/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCN(C(=O)OC(C)(C)C)C1)C(=O)[O-]) `REAL300004919372.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919372 none CC#CCC(NC(=O)C1CCN(C(=O)OC(C)(C)C)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 29, 11, 11, 1, 11, 1, 1, 1, 1, 1, 2, 2, 9, 11, 12, 11, 1, 29, 43, 43, 67, 67, 67, 67, 67, 29, 11, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1] 201 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 45, 44, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 355 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919372 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919372 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919372/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919372 Building REAL300004919373 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919373' /scratch/stefan/7775247/working/building/REAL300004919373 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919373 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919373/0 /scratch/stefan/7775247/working/building/REAL300004919373 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/373 `/scratch/stefan/7775247/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Cl)=C(Br)N1)C(=O)[O-]) `REAL300004919373.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919373 none CC#CCC(NC(=O)C1=CC(Cl)=C(Br)N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'Br', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 17, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 35, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 35, 49, 49, 69, 69, 69, 69, 69, 35, 11, 1, 1] 69 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 25, 26] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 337 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919373 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919373 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919373/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919373 Building REAL300004919374 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919374' /scratch/stefan/7775247/working/building/REAL300004919374 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919374 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919374/0 /scratch/stefan/7775247/working/building/REAL300004919374 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/374 `/scratch/stefan/7775247/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=NN(C2=CC=CC=C2)N=C1)C(=O)[O-]) `REAL300004919374.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919374 none CC#CCC(NC(=O)CC1=NN(C2=CC=CC=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 95, 42, 42, 7, 42, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 1, 95, 139, 139, 201, 201, 201, 201, 201, 95, 42, 7, 7, 4, 4, 2, 4, 4, 1] 201 rigid atoms, others: [37, 8, 9, 10, 11, 12, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 1014 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919374 none CC#CCC(NC(=O)CC1=NN(C2=CC=CC=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 111, 55, 55, 14, 55, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 111, 150, 150, 201, 201, 201, 201, 201, 111, 55, 14, 14, 1, 1, 1, 1, 1, 4] 201 rigid atoms, others: [32, 33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37]) total number of confs: 1002 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919374 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919374 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919374/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919374 Building REAL300004919375 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919375' /scratch/stefan/7775247/working/building/REAL300004919375 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919375 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919375/0 /scratch/stefan/7775247/working/building/REAL300004919375 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/375 `/scratch/stefan/7775247/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CN(CC1CC1)C(=O)OC(C)(C)C)C(=O)[O-]) `REAL300004919375.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919375 none CC#CCC(NC(=O)CN(CC1CC1)C(=O)OC(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 8, 5, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 91, 67, 67, 31, 67, 14, 7, 1, 1, 1, 1, 14, 22, 22, 41, 41, 41, 41, 91, 101, 101, 107, 107, 107, 107, 107, 91, 67, 31, 31, 7, 7, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41] 201 rigid atoms, others: [35, 36, 37, 38, 39, 10, 11, 12, 13] 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, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 542 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919375 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919375 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919375/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919375 Building REAL300004919376 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919376' /scratch/stefan/7775247/working/building/REAL300004919376 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919376 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919376/0 /scratch/stefan/7775247/working/building/REAL300004919376 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/376 `/scratch/stefan/7775247/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCN(C(=O)OC(C)(C)C)C(C)C)C(=O)[O-]) `REAL300004919376.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.0.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.0.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.0.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919376 none CC#CCC(NC(=O)CCN(C(=O)OC(C)(C)C)C(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 4, 4, 3, 4, 2, 1, 1, 1, 2, 2, 5, 5, 5, 5, 1, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 3, 3, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2] 7 rigid atoms, others: [9, 10, 11, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 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: 56 number of broken/clashed sets: 6 ./output.0.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919376 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919376 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919376/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919376 Building REAL300004919377 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919377' /scratch/stefan/7775247/working/building/REAL300004919377 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919377 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919377/0 /scratch/stefan/7775247/working/building/REAL300004919377 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/377 `/scratch/stefan/7775247/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC([N+](=O)[O-])=CC=C1NC)C(=O)[O-]) `REAL300004919377.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919377 none CC#CCC(NC(=O)C1=CC([N+](=O)[O-])=CC=C1NC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 8, 11, 11, 1, 1, 1, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 2, 2, 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: [112, 112, 112, 38, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 38, 62, 62, 112, 112, 112, 112, 112, 38, 13, 1, 1, 1, 10, 10, 10, 10] 118 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 554 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919377 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919377 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919377/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919377 Building REAL300004919378 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919378' /scratch/stefan/7775247/working/building/REAL300004919378 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919378 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919378/0 /scratch/stefan/7775247/working/building/REAL300004919378 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/378 `/scratch/stefan/7775247/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC(Cl)=C(OC(C)C)C(OC)=C1)C(=O)[O-]) `REAL300004919378.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919378 none CC#CCC(NC(=O)C=CC1=CC(Cl)=C(OC(C)C)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 5, 1, 12, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 39, 20, 20, 5, 20, 5, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1, 4, 1, 39, 65, 65, 85, 85, 85, 85, 85, 39, 20, 5, 5, 1, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 1] 201 rigid atoms, others: [35, 9, 10, 11, 12, 13, 14, 15, 19, 20, 46, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 489 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919378 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919378 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919378/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919378 Building REAL300004919379 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919379' /scratch/stefan/7775247/working/building/REAL300004919379 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919379 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919379/0 /scratch/stefan/7775247/working/building/REAL300004919379 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/379 `/scratch/stefan/7775247/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(Cl)N(CC(C)C)N=C1C)C(=O)[O-]) `REAL300004919379.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919379 none CC#CCC(NC(=O)C1=C(Cl)N(CC(C)C)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 16, 8, 5, 5, 5, 5, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 26, 6, 6, 1, 6, 1, 1, 1, 1, 1, 4, 7, 7, 1, 1, 1, 26, 43, 43, 78, 78, 78, 78, 78, 26, 7, 4, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 2] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 410 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919379 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919379 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919379/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919379 Building REAL300004919380 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919380' /scratch/stefan/7775247/working/building/REAL300004919380 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919380 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919380/0 /scratch/stefan/7775247/working/building/REAL300004919380 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/380 `/scratch/stefan/7775247/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(S(=O)(=O)N(C)C)=CC=C1C)C(=O)[O-]) `REAL300004919380.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919380 none CC#CCC(NC(=O)C1=CC(S(=O)(=O)N(C)C)=CC=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 24, 10, 10, 1, 10, 1, 1, 1, 1, 9, 9, 9, 16, 16, 1, 1, 1, 1, 24, 38, 38, 55, 55, 55, 55, 55, 24, 10, 1, 16, 16, 16, 16, 16, 16, 1, 1, 2, 2, 2] 201 rigid atoms, others: [38, 6, 39, 8, 9, 10, 11, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 336 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919380 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919380 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919380/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919380 Building REAL300004919381 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919381' /scratch/stefan/7775247/working/building/REAL300004919381 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919381 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919381/0 /scratch/stefan/7775247/working/building/REAL300004919381 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 381) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/381 `/scratch/stefan/7775247/working/3D/381' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC)C(S(=O)(=O)N(C)C)=C1)C(=O)[O-]) `REAL300004919381.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919381 none CC#CCC(NC(=O)C1=CC=C(OC)C(S(=O)(=O)N(C)C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 14, 11, 11, 8, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 3, 1, 1, 9, 9, 9, 13, 13, 1, 17, 29, 29, 49, 49, 49, 49, 49, 17, 5, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 13, 1] 201 rigid atoms, others: [32, 33, 43, 6, 8, 9, 10, 11, 12, 14, 15, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 291 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919381 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919381 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919381/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919381 Building REAL300004919382 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919382' /scratch/stefan/7775247/working/building/REAL300004919382 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919382 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919382/0 /scratch/stefan/7775247/working/building/REAL300004919382 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/382 `/scratch/stefan/7775247/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)N2CCCC(C)C2)C=C1)C(=O)[O-]) `REAL300004919382.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919382 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)N2CCCC(C)C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 8, 8, 8, 33, 33, 33, 33, 33, 33, 1, 1, 9, 14, 14, 28, 28, 28, 28, 28, 9, 3, 1, 1, 33, 33, 33, 32, 33, 33, 32, 33, 33, 33, 33, 33, 1, 1] 201 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 48, 49, 22, 23] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919382 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)N2CCCC(C)C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 59, 59, 6, 59, 6, 32, 32, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 32, 32, 132, 161, 161, 201, 201, 201, 201, 201, 132, 59, 32, 32, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 32, 32] 201 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 12, 46, 15, 16, 17, 18, 19, 20, 21, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 48, 49]) total number of confs: 1034 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919382 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919382 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919382/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919382 Building REAL300004919383 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919383' /scratch/stefan/7775247/working/building/REAL300004919383 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919383 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919383/0 /scratch/stefan/7775247/working/building/REAL300004919383 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 383) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/383 `/scratch/stefan/7775247/working/3D/383' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CC=C(Cl)C=C2)S1)C(=O)[O-]) `REAL300004919383.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919383 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(Cl)C=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 40, 13, 13, 1, 13, 1, 1, 1, 1, 1, 6, 6, 1, 1, 6, 6, 1, 40, 61, 61, 84, 84, 84, 84, 84, 40, 13, 1, 1, 6, 6, 6, 6] 157 rigid atoms, others: [6, 8, 9, 10, 11, 12, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 439 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919383 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(Cl)C=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [157, 157, 157, 106, 61, 61, 6, 61, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 106, 128, 128, 157, 157, 157, 157, 157, 106, 61, 6, 6, 1, 1, 1, 1] 157 rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 691 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919383 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919383 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919383/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919383 Building REAL300004919384 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919384' /scratch/stefan/7775247/working/building/REAL300004919384 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919384 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919384/0 /scratch/stefan/7775247/working/building/REAL300004919384 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/384 `/scratch/stefan/7775247/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(Br)C(Cl)=C1)C(=O)[O-]) `REAL300004919384.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919384 none CC#CCC(NC(=O)C=CC1=CC=C(Br)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 17, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [173, 173, 173, 101, 45, 45, 6, 45, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 101, 130, 130, 173, 173, 173, 173, 173, 101, 45, 6, 6, 1, 1, 1] 173 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 789 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919384 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919384 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919384/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919384 Building REAL300004919385 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919385' /scratch/stefan/7775247/working/building/REAL300004919385 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919385 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919385/0 /scratch/stefan/7775247/working/building/REAL300004919385 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 385) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/385 `/scratch/stefan/7775247/working/3D/385' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC(OC)=C(OC)C=C1OC)C(=O)[O-]) `REAL300004919385.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919385 none CC#CCC(NC(=O)C=CC1=CC(OC)=C(OC)C=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 50, 33, 33, 9, 33, 9, 1, 1, 1, 1, 1, 3, 1, 1, 3, 1, 1, 1, 3, 50, 74, 74, 107, 107, 107, 107, 107, 50, 33, 9, 9, 1, 3, 3, 3, 4, 4, 4, 1, 3, 3, 3] 201 rigid atoms, others: [34, 9, 10, 11, 12, 13, 15, 16, 18, 19, 20, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 557 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919385 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919385 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919385/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919385 Building REAL300004919386 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919386' /scratch/stefan/7775247/working/building/REAL300004919386 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919386 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919386/0 /scratch/stefan/7775247/working/building/REAL300004919386 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/386 `/scratch/stefan/7775247/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2)N=C1C)C(=O)[O-]) `REAL300004919386.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919386 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 29, 10, 10, 1, 10, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 1, 1, 29, 41, 41, 58, 58, 58, 58, 58, 29, 10, 4, 4, 2, 4, 4, 2, 2, 2] 58 rigid atoms, others: [6, 8, 9, 10, 11, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 290 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: REAL300004919386 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 34, 16, 16, 4, 16, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 34, 46, 46, 58, 58, 58, 58, 58, 34, 16, 1, 1, 1, 1, 1, 4, 4, 4] 58 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37]) total number of confs: 278 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919386 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919386 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919386/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919386 Building REAL300004919387 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919387' /scratch/stefan/7775247/working/building/REAL300004919387 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919387 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919387/0 /scratch/stefan/7775247/working/building/REAL300004919387 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 387) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/387 `/scratch/stefan/7775247/working/3D/387' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(COC(C)C)C=C1)C(=O)[O-]) `REAL300004919387.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919387 none CC#CCC(NC(=O)C1=CC=C(COC(C)C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 5, 12, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 8, 33, 47, 47, 1, 1, 7, 11, 11, 21, 21, 21, 21, 21, 7, 3, 1, 1, 8, 8, 47, 47, 47, 47, 47, 47, 47, 1, 1] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 17, 18, 41, 40, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919387 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919387 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919387/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919387 Building REAL300004919388 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919388' /scratch/stefan/7775247/working/building/REAL300004919388 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919388 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919388/0 /scratch/stefan/7775247/working/building/REAL300004919388 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/388 `/scratch/stefan/7775247/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C2CC2)=NN1C1=CC=CC=C1)C(=O)[O-]) `REAL300004919388.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919388 none CC#CCC(NC(=O)C1=CC(C2CC2)=NN1C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 29, 12, 12, 1, 12, 1, 1, 1, 1, 13, 13, 1, 1, 1, 5, 5, 2, 5, 5, 29, 50, 50, 94, 94, 94, 94, 94, 29, 12, 1, 13, 13, 13, 13, 13, 5, 5, 3, 5, 5] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 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]) total number of confs: 486 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919388 none CC#CCC(NC(=O)C1=CC(C2CC2)=NN1C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 111, 42, 20, 20, 5, 20, 5, 5, 5, 5, 38, 38, 5, 1, 1, 1, 1, 1, 1, 1, 42, 69, 69, 111, 111, 111, 111, 111, 42, 20, 5, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) 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: REAL300004919388 none CC#CCC(NC(=O)C1=CC(C2CC2)=NN1C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [196, 196, 196, 119, 73, 73, 13, 73, 13, 13, 1, 1, 1, 1, 13, 13, 13, 38, 38, 14, 38, 38, 119, 150, 150, 196, 196, 196, 196, 196, 119, 73, 13, 1, 1, 1, 1, 1, 38, 38, 22, 38, 38] 201 rigid atoms, others: [33, 34, 35, 36, 37, 10, 11, 12, 13] 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, 38, 39, 40, 41, 42]) total number of confs: 957 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919388 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919388 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919388/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919388 Building REAL300004919389 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919389' /scratch/stefan/7775247/working/building/REAL300004919389 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919389 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919389/0 /scratch/stefan/7775247/working/building/REAL300004919389 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 389) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/389 `/scratch/stefan/7775247/working/3D/389' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=CC=C(OC)C=C2C=C1)C(=O)[O-]) `REAL300004919389.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919389 none CC#CCC(NC(=O)C1=CC2=CC=C(OC)C=C2C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 27, 42, 42, 85, 85, 85, 85, 85, 27, 7, 1, 1, 1, 3, 3, 3, 1, 1, 1] 114 rigid atoms, others: [32, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 34, 15, 33, 35, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 392 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919389 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919389 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919389/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919389 Building REAL300004919390 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919390' /scratch/stefan/7775247/working/building/REAL300004919390 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919390 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919390/0 /scratch/stefan/7775247/working/building/REAL300004919390 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/390 `/scratch/stefan/7775247/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CSC1=CC=C(OCC)C=C1)C(=O)[O-]) `REAL300004919390.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919390 none CC#CCC(NC(=O)CSC1=CC=C(OCC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 14, 1, 1, 1, 1, 12, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 104, 61, 39, 39, 14, 39, 4, 1, 1, 1, 1, 1, 1, 6, 14, 1, 1, 61, 88, 88, 104, 104, 104, 104, 104, 61, 39, 14, 14, 1, 1, 14, 14, 15, 15, 15, 1, 1] 201 rigid atoms, others: [32, 38, 39, 9, 10, 11, 12, 13, 14, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 601 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919390 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919390 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919390/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919390 Building REAL300004919391 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919391' /scratch/stefan/7775247/working/building/REAL300004919391 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919391 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919391/0 /scratch/stefan/7775247/working/building/REAL300004919391 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/391 `/scratch/stefan/7775247/working/3D/391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CC=C(Cl)C=C2Cl)O1)C(=O)[O-]) `REAL300004919391.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919391 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(Cl)C=C2Cl)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 31, 10, 10, 1, 10, 1, 1, 1, 1, 1, 10, 10, 1, 2, 10, 10, 10, 1, 31, 49, 49, 77, 77, 77, 77, 77, 31, 10, 1, 1, 10, 10, 10] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 395 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919391 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(Cl)C=C2Cl)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 16, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 126, 57, 57, 10, 57, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 126, 152, 152, 201, 201, 201, 201, 201, 126, 57, 10, 10, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 890 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919391 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919391 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919391/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919391 Building REAL300004919392 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919392' /scratch/stefan/7775247/working/building/REAL300004919392 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919392 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919392/0 /scratch/stefan/7775247/working/building/REAL300004919392 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/392 `/scratch/stefan/7775247/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC=CC(OC)=C1OC)C(=O)[O-]) `REAL300004919392.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919392 none CC#CCC(NC(=O)CCC1=CC=CC(OC)=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 2, 2, 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: [6, 6, 6, 5, 5, 5, 5, 5, 4, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 4, 5, 5, 5, 6, 6, 6, 6, 6, 5, 5, 5, 5, 4, 4, 1, 1, 1, 3, 3, 3, 4, 4, 4] 9 rigid atoms, others: [34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919392 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919392 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919392/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919392 Building REAL300004919393 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919393' /scratch/stefan/7775247/working/building/REAL300004919393 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919393 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919393/0 /scratch/stefan/7775247/working/building/REAL300004919393 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 393) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/393 `/scratch/stefan/7775247/working/3D/393' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C(C)(C)C)C([N+](=O)[O-])=C1)C(=O)[O-]) `REAL300004919393.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919393 none CC#CCC(NC(=O)C1=CC=C(C(C)(C)C)C([N+](=O)[O-])=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 1, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 2, 2, 1, 27, 37, 37, 64, 64, 64, 64, 64, 27, 7, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1] 64 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 16, 17, 20, 42, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 305 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919393 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919393 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919393/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919393 Building REAL300004919394 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919394' /scratch/stefan/7775247/working/building/REAL300004919394 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919394 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919394/0 /scratch/stefan/7775247/working/building/REAL300004919394 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/394 `/scratch/stefan/7775247/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C2OCCCOC2=C1)C(=O)[O-]) `REAL300004919394.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919394 none CC#CCC(NC(=O)C1=CC=C2OCCCOC2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 28, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 39, 39, 68, 68, 68, 68, 68, 28, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1] 68 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 311 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919394 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919394 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919394/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919394 Building REAL300004919395 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919395' /scratch/stefan/7775247/working/building/REAL300004919395 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919395 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919395/0 /scratch/stefan/7775247/working/building/REAL300004919395 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/395 `/scratch/stefan/7775247/working/3D/395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1(CC2=NC3=CC=CC=C3S2)CCCCC1)C(=O)[O-]) `REAL300004919395.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919395 none CC#CCC(NC(=O)CC1(CC2=NC3=CC=CC=C3S2)CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 16, 9, 9, 8, 9, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 16, 16, 16, 19, 19, 19, 19, 19, 16, 9, 8, 8, 5, 5, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 21 rigid atoms, others: [8, 9, 10, 43, 44, 45, 46, 47, 48, 49, 50, 51, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 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: 101 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919395 none CC#CCC(NC(=O)CC1(CC2=NC3=CC=CC=C3S2)CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 14, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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, 19, 12, 12, 11, 12, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 19, 19, 19, 21, 21, 21, 21, 21, 19, 12, 11, 11, 5, 5, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 21 rigid atoms, others: [39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 89 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919395 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919395 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919395/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919395 Building REAL300004919396 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919396' /scratch/stefan/7775247/working/building/REAL300004919396 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919396 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919396/0 /scratch/stefan/7775247/working/building/REAL300004919396 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/396 `/scratch/stefan/7775247/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=C(C=C1[N+](=O)[O-])OCO2)C(=O)[O-]) `REAL300004919396.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919396 none CC#CCC(NC(=O)C1=CC2=C(C=C1[N+](=O)[O-])OCO2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'C.3', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 11, 11, 12, 5, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 15, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 15, 22, 22, 39, 39, 39, 39, 39, 15, 6, 1, 1, 1, 1] 39 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919396 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919396 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919396/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919396 Building REAL300004919397 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919397' /scratch/stefan/7775247/working/building/REAL300004919397 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919397 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919397/0 /scratch/stefan/7775247/working/building/REAL300004919397 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/397 `/scratch/stefan/7775247/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CSC1=CC=C(OC)C=C1)C(=O)[O-]) `REAL300004919397.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919397 none CC#CCC(NC(=O)CSC1=CC=C(OC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 14, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 147, 107, 66, 66, 20, 66, 4, 1, 1, 1, 1, 1, 1, 3, 1, 1, 107, 129, 129, 147, 147, 147, 147, 147, 107, 66, 20, 20, 1, 1, 3, 3, 3, 1, 1] 201 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 701 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919397 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919397 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919397/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919397 Building REAL300004919398 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919398' /scratch/stefan/7775247/working/building/REAL300004919398 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919398 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919398/0 /scratch/stefan/7775247/working/building/REAL300004919398 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/398 `/scratch/stefan/7775247/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2SCCCS2)C=C1)C(=O)[O-]) `REAL300004919398.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919398 none CC#CCC(NC(=O)C1=CC=C(C2SCCCS2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 5, 14, 5, 5, 5, 14, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [39, 39, 39, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1, 12, 20, 20, 39, 39, 39, 39, 39, 12, 4, 1, 1, 13, 13, 13, 13, 13, 13, 13, 1, 1] 90 rigid atoms, others: [6, 39, 8, 9, 10, 11, 12, 40, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919398 none CC#CCC(NC(=O)C1=CC=C(C2SCCCS2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 5, 14, 5, 5, 5, 14, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 46, 19, 19, 4, 19, 1, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 46, 59, 59, 90, 90, 90, 90, 90, 46, 19, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13] 90 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40]) total number of confs: 437 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919398 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919398 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919398/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919398 Building REAL300004919399 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919399' /scratch/stefan/7775247/working/building/REAL300004919399 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919399 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919399/0 /scratch/stefan/7775247/working/building/REAL300004919399 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 399) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/399 `/scratch/stefan/7775247/working/3D/399' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC=C(C)C=C1Br)C(=O)[O-]) `REAL300004919399.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919399 none CC#CCC(NC(=O)COC1=CC=C(C)C=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [180, 180, 180, 155, 116, 116, 37, 116, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 155, 165, 165, 180, 180, 180, 180, 180, 155, 116, 37, 37, 1, 1, 2, 2, 2, 1] 180 rigid atoms, others: [35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 741 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919399 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919399 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919399/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919399 Building REAL300004919400 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919400' /scratch/stefan/7775247/working/building/REAL300004919400 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919400 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919400/0 /scratch/stefan/7775247/working/building/REAL300004919400 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/400 `/scratch/stefan/7775247/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)(C)OC1=CC=C(OCC)C=C1)C(=O)[O-]) `REAL300004919400.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919400 none CC#CCC(NC(=O)C(C)(C)OC1=CC=C(OCC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 12, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 110, 72, 37, 37, 13, 37, 4, 13, 13, 1, 1, 1, 1, 1, 1, 6, 17, 1, 1, 72, 88, 88, 110, 110, 110, 110, 110, 72, 37, 13, 13, 13, 13, 13, 13, 1, 1, 17, 17, 17, 17, 17, 1, 1] 201 rigid atoms, others: [45, 37, 38, 44, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43]) total number of confs: 593 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919400 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919400 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919400/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919400 Building REAL300004919401 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919401' /scratch/stefan/7775247/working/building/REAL300004919401 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919401 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919401/0 /scratch/stefan/7775247/working/building/REAL300004919401 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/401 `/scratch/stefan/7775247/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCN(C(=O)OC(C)(C)C)CC1)C(=O)[O-]) `REAL300004919401.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919401 none CC#CCC(NC(=O)C1CCN(C(=O)OC(C)(C)C)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 29, 12, 12, 1, 12, 1, 1, 1, 1, 1, 5, 5, 12, 13, 13, 13, 1, 1, 29, 48, 48, 61, 61, 61, 61, 61, 29, 13, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 45, 46, 47, 48, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 371 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919401 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919401 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919401/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919401 Building REAL300004919402 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919402' /scratch/stefan/7775247/working/building/REAL300004919402 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919402 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919402/0 /scratch/stefan/7775247/working/building/REAL300004919402 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/402 `/scratch/stefan/7775247/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(NC(=O)OC(C)(C)C)=C1)C(=O)[O-]) `REAL300004919402.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919402 none CC#CCC(NC(=O)C1=CC=CC(NC(=O)OC(C)(C)C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 9, 12, 12, 15, 15, 15, 15, 1, 13, 18, 18, 31, 31, 31, 31, 31, 13, 5, 1, 1, 1, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1] 201 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 45, 21] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919402 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919402 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919402/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919402 Building REAL300004919403 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919403' /scratch/stefan/7775247/working/building/REAL300004919403 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919403 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919403/0 /scratch/stefan/7775247/working/building/REAL300004919403 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 403) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/403 `/scratch/stefan/7775247/working/3D/403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC=C(Cl)C2=CC=CC=C12)C(=O)[O-]) `REAL300004919403.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919403 none CC#CCC(NC(=O)COC1=CC=C(Cl)C2=CC=CC=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 126, 126, 35, 126, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 181, 185, 185, 201, 201, 201, 201, 201, 181, 126, 35, 35, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 803 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919403 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919403 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919403/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919403 Building REAL300004919404 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919404' /scratch/stefan/7775247/working/building/REAL300004919404 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919404 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919404/0 /scratch/stefan/7775247/working/building/REAL300004919404 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/404 `/scratch/stefan/7775247/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(NC(=O)OC(C)(C)C)C=C1)C(=O)[O-]) `REAL300004919404.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919404 none CC#CCC(NC(=O)C1=CC=C(NC(=O)OC(C)(C)C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 9, 16, 16, 28, 32, 32, 32, 1, 1, 8, 13, 13, 25, 25, 25, 25, 25, 8, 3, 1, 1, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 45, 44, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919404 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919404 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919404/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919404 Building REAL300004919405 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919405' /scratch/stefan/7775247/working/building/REAL300004919405 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919405 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919405/0 /scratch/stefan/7775247/working/building/REAL300004919405 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/405 `/scratch/stefan/7775247/working/3D/405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CNC(=O)OC(C)(C)C)C1=CC=CC=C1)C(=O)[O-]) `REAL300004919405.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919405 none CC#CCC(NC(=O)C(CNC(=O)OC(C)(C)C)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 10, 3, 3, 2, 3, 1, 2, 5, 11, 17, 17, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 10, 14, 14, 16, 16, 16, 16, 16, 10, 3, 2, 5, 5, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1] 44 rigid atoms, others: [51, 8, 50, 47, 48, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919405 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919405 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919405/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919405 Building REAL300004919406 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919406' /scratch/stefan/7775247/working/building/REAL300004919406 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919406 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919406/0 /scratch/stefan/7775247/working/building/REAL300004919406 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/406 `/scratch/stefan/7775247/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=C(OC)C([N+](=O)[O-])=C1)C(=O)[O-]) `REAL300004919406.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919406 none CC#CCC(NC(=O)CC1=CC=C(OC)C([N+](=O)[O-])=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 12, 5, 1, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [149, 149, 149, 51, 16, 16, 6, 16, 1, 1, 1, 1, 1, 1, 4, 1, 1, 2, 2, 1, 51, 90, 90, 149, 149, 149, 149, 149, 51, 16, 6, 6, 1, 1, 4, 4, 4, 1] 201 rigid atoms, others: [32, 33, 37, 8, 9, 10, 11, 12, 13, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 750 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919406 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919406 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919406/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919406 Building REAL300004919407 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919407' /scratch/stefan/7775247/working/building/REAL300004919407 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919407 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919407/0 /scratch/stefan/7775247/working/building/REAL300004919407 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 407) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/407 `/scratch/stefan/7775247/working/3D/407' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC=CC=C1OCC(F)(F)F)C(=O)[O-]) `REAL300004919407.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919407 none CC#CCC(NC(=O)COC1=CC=CC=C1OCC(F)(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 47, 35, 35, 21, 35, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9, 30, 30, 30, 30, 47, 68, 68, 89, 89, 89, 89, 89, 47, 35, 21, 21, 1, 1, 1, 1, 30, 30] 201 rigid atoms, others: [34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 16] 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, 38, 39]) total number of confs: 554 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919407 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919407 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919407/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919407 Building REAL300004919408 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919408' /scratch/stefan/7775247/working/building/REAL300004919408 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919408 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919408/0 /scratch/stefan/7775247/working/building/REAL300004919408 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/408 `/scratch/stefan/7775247/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CS(=O)(=O)CCCCC)C(=O)[O-]) `REAL300004919408.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.0.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.0.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.0.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919408 none CC#CCC(NC(=O)CS(=O)(=O)CCCCC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 14, 11, 11, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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: [11, 11, 11, 11, 6, 6, 1, 6, 1, 1, 5, 5, 5, 10, 13, 18, 18, 11, 12, 12, 11, 11, 11, 11, 11, 11, 6, 1, 1, 10, 10, 13, 13, 18, 18, 18, 18, 18, 18, 18] 31 rigid atoms, others: [8, 9, 27, 28, 6] set([0, 1, 2, 3, 4, 5, 7, 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.0.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919408 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919408 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919408/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919408 Building REAL300004919409 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919409' /scratch/stefan/7775247/working/building/REAL300004919409 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919409 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919409/0 /scratch/stefan/7775247/working/building/REAL300004919409 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 409) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/409 `/scratch/stefan/7775247/working/3D/409' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Br)=CC2=CC=CC=C21)C(=O)[O-]) `REAL300004919409.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919409 none CC#CCC(NC(=O)C1=CC(Br)=CC2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 36, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 54, 54, 90, 90, 90, 90, 90, 36, 9, 1, 1, 1, 1, 1, 1] 90 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 418 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919409 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919409 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919409/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919409 Building REAL300004919410 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919410' /scratch/stefan/7775247/working/building/REAL300004919410 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919410 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919410/0 /scratch/stefan/7775247/working/building/REAL300004919410 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/410 `/scratch/stefan/7775247/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C)CCN(C(=O)OC(C)(C)C)CC1)C(=O)[O-]) `REAL300004919410.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919410 none CC#CCC(NC(=O)C1(C)CCN(C(=O)OC(C)(C)C)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 23, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 6, 6, 14, 15, 15, 15, 1, 1, 23, 37, 37, 62, 62, 62, 62, 62, 23, 7, 2, 2, 2, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 48, 49, 50, 51, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 354 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919410 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919410 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919410/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919410 Building REAL300004919411 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919411' /scratch/stefan/7775247/working/building/REAL300004919411 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919411 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919411/0 /scratch/stefan/7775247/working/building/REAL300004919411 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 411) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/411 `/scratch/stefan/7775247/working/3D/411' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)(C)C1=CC=CC=C1Cl)C(=O)[O-]) `REAL300004919411.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919411 none CC#CCC(NC(=O)C(C)(C)C1=CC=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 46, 15, 15, 3, 15, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 46, 67, 67, 114, 114, 114, 114, 114, 46, 15, 3, 3, 3, 4, 4, 4, 1, 1, 1, 1] 114 rigid atoms, others: [34, 35, 36, 37, 8, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 547 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919411 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919411 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919411/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919411 Building REAL300004919412 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919412' /scratch/stefan/7775247/working/building/REAL300004919412 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919412 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919412/0 /scratch/stefan/7775247/working/building/REAL300004919412 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/412 `/scratch/stefan/7775247/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(I)=C1C)C(=O)[O-]) `REAL300004919412.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919412 none CC#CCC(NC(=O)C1=CC=CC(I)=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 18, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 39, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 39, 52, 52, 79, 79, 79, 79, 79, 39, 10, 1, 1, 1, 2, 2, 2] 79 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 376 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919412 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919412 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919412/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919412 Building REAL300004919413 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919413' /scratch/stefan/7775247/working/building/REAL300004919413 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919413 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919413/0 /scratch/stefan/7775247/working/building/REAL300004919413 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/413 `/scratch/stefan/7775247/working/3D/413' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(Br)C=C1[N+](=O)[O-])C(=O)[O-]) `REAL300004919413.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919413 none CC#CCC(NC(=O)C1=CC=C(Br)C=C1[N+](=O)[O-])C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 17, 1, 1, 8, 11, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 19, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 19, 25, 25, 39, 39, 39, 39, 39, 19, 6, 1, 1, 1] 39 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919413 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919413 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919413/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919413 Building REAL300004919414 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919414' /scratch/stefan/7775247/working/building/REAL300004919414 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919414 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919414/0 /scratch/stefan/7775247/working/building/REAL300004919414 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/414 `/scratch/stefan/7775247/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC(NC(=O)OC(C)(C)C)C1=CC=CC=C1)C(=O)[O-]) `REAL300004919414.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919414 none CC#CCC(NC(=O)CCC(NC(=O)OC(C)(C)C)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 30, 20, 20, 11, 20, 7, 4, 1, 4, 8, 14, 14, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 30, 32, 32, 37, 37, 37, 37, 37, 30, 20, 11, 11, 7, 7, 4, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1] 61 rigid atoms, others: [51, 54, 10, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 227 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919414 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919414 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919414/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919414 Building REAL300004919415 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919415' /scratch/stefan/7775247/working/building/REAL300004919415 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919415 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919415/0 /scratch/stefan/7775247/working/building/REAL300004919415 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 415) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/415 `/scratch/stefan/7775247/working/3D/415' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=C(C)C=C2F)C2=C1CCC2)C(=O)[O-]) `REAL300004919415.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919415 none CC#CCC(NC(=O)C1=NN(C2=CC=C(C)C=C2F)C2=C1CCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 15, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [76, 76, 76, 36, 12, 12, 1, 12, 1, 1, 1, 1, 10, 10, 1, 9, 10, 10, 10, 1, 1, 1, 1, 1, 36, 49, 49, 76, 76, 76, 76, 76, 36, 12, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1] 178 rigid atoms, others: [41, 43, 6, 8, 9, 10, 11, 44, 45, 40, 19, 20, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 383 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919415 none CC#CCC(NC(=O)C1=NN(C2=CC=C(C)C=C2F)C2=C1CCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 15, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [178, 178, 178, 102, 46, 46, 10, 46, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 102, 132, 132, 178, 178, 178, 178, 178, 102, 46, 1, 1, 2, 2, 2, 1, 10, 10, 10, 10, 10, 10] 178 rigid atoms, others: [34, 35, 39, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 850 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919415 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919415 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919415/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919415 Building REAL300004919416 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919416' /scratch/stefan/7775247/working/building/REAL300004919416 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919416 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919416/0 /scratch/stefan/7775247/working/building/REAL300004919416 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/416 `/scratch/stefan/7775247/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=C(C)CC1=CC=CC=C1OC)C(=O)[O-]) `REAL300004919416.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919416 none CC#CCC(NC(=O)C=C(C)CC1=CC=CC=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 183, 86, 56, 56, 13, 56, 13, 5, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 86, 133, 133, 183, 183, 183, 183, 183, 86, 56, 13, 13, 13, 13, 5, 5, 1, 1, 1, 1, 3, 3, 3] 201 rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42]) total number of confs: 970 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919416 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919416 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919416/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919416 Building REAL300004919417 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919417' /scratch/stefan/7775247/working/building/REAL300004919417 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919417 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919417/0 /scratch/stefan/7775247/working/building/REAL300004919417 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/417 `/scratch/stefan/7775247/working/3D/417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)SC1=CC=CC=C1S(=O)(=O)CCC)C(=O)[O-]) `REAL300004919417.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919417 none CC#CCC(NC(=O)C(C)SC1=CC=CC=C1S(=O)(=O)CCC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 14, 1, 1, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 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, 7, 6, 6, 4, 6, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 7, 8, 8, 10, 10, 10, 10, 10, 7, 6, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5] 16 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 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, 47]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919417 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919417 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919417/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919417 Building REAL300004919418 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919418' /scratch/stefan/7775247/working/building/REAL300004919418 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919418 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919418/0 /scratch/stefan/7775247/working/building/REAL300004919418 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/418 `/scratch/stefan/7775247/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2)C=C1OCC(C)C)C(=O)[O-]) `REAL300004919418.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919418 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2)C=C1OCC(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 7, 7, 1, 7, 1, 1, 1, 1, 3, 3, 2, 3, 3, 1, 1, 1, 10, 36, 41, 53, 19, 31, 31, 50, 50, 50, 50, 50, 19, 7, 3, 3, 2, 3, 3, 1, 36, 36, 53, 53, 53, 53, 53, 53, 53] 201 rigid atoms, others: [6, 39, 8, 9, 10, 11, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 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: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919418 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2)C=C1OCC(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 20, 9, 9, 3, 9, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 13, 39, 43, 55, 20, 32, 32, 51, 51, 51, 51, 51, 20, 9, 1, 1, 1, 1, 1, 3, 39, 39, 55, 55, 55, 55, 55, 55, 55] 201 rigid atoms, others: [34, 35, 36, 37, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 539 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919418 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919418 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919418/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919418 Building REAL300004919419 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919419' /scratch/stefan/7775247/working/building/REAL300004919419 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919419 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919419/0 /scratch/stefan/7775247/working/building/REAL300004919419 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/419 `/scratch/stefan/7775247/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CC=C(OC)C=C2F)C=C1F)C(=O)[O-]) `REAL300004919419.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919419 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(OC)C=C2F)C=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 15, 1, 1, 15, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 22, 11, 11, 1, 11, 1, 1, 1, 1, 1, 7, 7, 2, 6, 13, 7, 7, 7, 1, 1, 1, 22, 37, 37, 56, 56, 56, 56, 56, 22, 11, 1, 1, 7, 7, 13, 13, 13, 7, 1] 201 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 316 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919419 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(OC)C=C2F)C=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 15, 1, 1, 15, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [162, 162, 162, 84, 46, 46, 7, 46, 6, 7, 7, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 7, 7, 7, 84, 127, 127, 162, 162, 162, 162, 162, 84, 46, 7, 7, 1, 1, 2, 2, 2, 1, 7] 201 rigid atoms, others: [36, 37, 41, 11, 12, 13, 14, 15, 16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 42]) total number of confs: 826 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919419 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919419 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919419/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919419 Building REAL300004919420 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919420' /scratch/stefan/7775247/working/building/REAL300004919420 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919420 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919420/0 /scratch/stefan/7775247/working/building/REAL300004919420 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/420 `/scratch/stefan/7775247/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=C(C)C=C2)C2=C1CCCC2)C(=O)[O-]) `REAL300004919420.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919420 none CC#CCC(NC(=O)C1=NN(C2=CC=C(C)C=C2)C2=C1CCCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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: [71, 71, 71, 33, 13, 13, 1, 12, 1, 1, 1, 1, 4, 4, 1, 1, 4, 4, 1, 1, 1, 1, 1, 1, 33, 45, 45, 71, 71, 71, 71, 71, 33, 13, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1] 104 rigid atoms, others: [41, 43, 6, 8, 9, 10, 11, 44, 45, 48, 18, 19, 20, 21, 22, 23, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 350 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: REAL300004919420 none CC#CCC(NC(=O)C1=NN(C2=CC=C(C)C=C2)C2=C1CCCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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: [104, 104, 104, 57, 25, 25, 4, 25, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 57, 74, 74, 104, 104, 104, 104, 104, 57, 25, 1, 1, 2, 2, 2, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4] 104 rigid atoms, others: [34, 35, 39, 40, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 505 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919420 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919420 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919420/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919420 Building REAL300004919421 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919421' /scratch/stefan/7775247/working/building/REAL300004919421 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919421 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919421/0 /scratch/stefan/7775247/working/building/REAL300004919421 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 421) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/421 `/scratch/stefan/7775247/working/3D/421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=NC2=CC(C(F)(F)F)=CC=C2S1)C(=O)[O-]) `REAL300004919421.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919421 none CC#CCC(NC(=O)CCC1=NC2=CC(C(F)(F)F)=CC=C2S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [85, 85, 85, 64, 42, 42, 12, 41, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 64, 70, 70, 85, 85, 85, 85, 85, 64, 42, 12, 12, 5, 5, 1, 1, 1] 85 rigid atoms, others: [37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 384 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919421 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919421 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919421/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919421 Building REAL300004919422 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919422' /scratch/stefan/7775247/working/building/REAL300004919422 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919422 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919422/0 /scratch/stefan/7775247/working/building/REAL300004919422 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/422 `/scratch/stefan/7775247/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)CC2=CC=CC=C2)=C1)C(=O)[O-]) `REAL300004919422.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919422 none CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)CC2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 19, 22, 22, 21, 22, 22, 1, 16, 24, 24, 39, 39, 39, 39, 39, 16, 5, 1, 1, 1, 19, 19, 22, 22, 22, 22, 22, 1] 201 rigid atoms, others: [34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 44, 23] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919422 none CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)CC2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 63, 63, 22, 63, 22, 21, 22, 22, 11, 3, 11, 11, 1, 1, 1, 1, 1, 1, 1, 22, 131, 163, 163, 201, 201, 201, 201, 201, 131, 63, 21, 22, 22, 3, 3, 1, 1, 1, 1, 1, 22] 201 rigid atoms, others: [39, 40, 41, 42, 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, 44]) total number of confs: 985 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919422 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919422 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919422/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919422 Building REAL300004919423 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919423' /scratch/stefan/7775247/working/building/REAL300004919423 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919423 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919423/0 /scratch/stefan/7775247/working/building/REAL300004919423 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 423) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/423 `/scratch/stefan/7775247/working/3D/423' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CC1C1=CC=CC2=CC=CC=C21)C(=O)[O-]) `REAL300004919423.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919423 none CC#CCC(NC(=O)C1CC1C1=CC=CC2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 115, 43, 13, 13, 1, 13, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 43, 67, 67, 115, 115, 115, 115, 115, 43, 13, 1, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6] 201 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 5, 7, 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]) total number of confs: 553 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919423 none CC#CCC(NC(=O)C1CC1C1=CC=CC2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 107, 47, 47, 6, 47, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 107, 141, 141, 201, 201, 201, 201, 201, 107, 47, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 940 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919423 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919423 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919423/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919423 Building REAL300004919424 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919424' /scratch/stefan/7775247/working/building/REAL300004919424 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919424 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919424/0 /scratch/stefan/7775247/working/building/REAL300004919424 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/424 `/scratch/stefan/7775247/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(CCC)N(C2=CC=CC(Cl)=C2)N=N1)C(=O)[O-]) `REAL300004919424.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919424 none CC#CCC(NC(=O)C1=C(CCC)N(C2=CC=CC(Cl)=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 39, 39, 19, 8, 8, 1, 8, 1, 1, 1, 5, 5, 1, 1, 9, 9, 6, 9, 9, 9, 1, 1, 19, 28, 28, 39, 39, 39, 39, 39, 19, 9, 5, 5, 5, 5, 5, 5, 5, 9, 9, 7, 9] 184 rigid atoms, others: [6, 8, 9, 10, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 229 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919424 none CC#CCC(NC(=O)C1=C(CCC)N(C2=CC=CC(Cl)=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 16, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [123, 123, 123, 73, 34, 34, 9, 34, 9, 9, 9, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 73, 90, 90, 123, 123, 123, 123, 123, 73, 34, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1] 184 rigid atoms, others: [40, 41, 42, 43, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 559 number of broken/clashed sets: 96 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919424 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919424 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919424/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919424 Building REAL300004919425 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919425' /scratch/stefan/7775247/working/building/REAL300004919425 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919425 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919425/0 /scratch/stefan/7775247/working/building/REAL300004919425 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/425 `/scratch/stefan/7775247/working/3D/425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC(C)=C(Cl)C(C)=C1)C(=O)[O-]) `REAL300004919425.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919425 none CC#CCC(NC(=O)COC1=CC(C)=C(Cl)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 12, 1, 1, 1, 5, 1, 16, 1, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 125, 79, 79, 20, 79, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 125, 161, 161, 201, 201, 201, 201, 201, 125, 79, 20, 20, 1, 2, 2, 2, 2, 2, 2, 1] 201 rigid atoms, others: [38, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37]) total number of confs: 990 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919425 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919425 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919425/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919425 Building REAL300004919426 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919426' /scratch/stefan/7775247/working/building/REAL300004919426 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919426 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919426/0 /scratch/stefan/7775247/working/building/REAL300004919426 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/426 `/scratch/stefan/7775247/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC=CC([N+](=O)[O-])=C1)C(=O)[O-]) `REAL300004919426.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919426 none CC#CCC(NC(=O)CCC1=CC=CC([N+](=O)[O-])=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 101, 50, 51, 11, 50, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 101, 139, 139, 201, 201, 201, 201, 201, 101, 51, 11, 11, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 980 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919426 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919426 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919426/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919426 Building REAL300004919427 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919427' /scratch/stefan/7775247/working/building/REAL300004919427 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919427 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919427/0 /scratch/stefan/7775247/working/building/REAL300004919427 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/427 `/scratch/stefan/7775247/working/3D/427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC2=CC=CC=C2)O1)C(=O)[O-]) `REAL300004919427.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919427 none CC#CCC(NC(=O)C1=CC=C(OC2=CC=CC=C2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 22, 8, 9, 1, 9, 1, 1, 1, 1, 1, 13, 30, 30, 13, 30, 30, 1, 22, 36, 36, 62, 62, 62, 62, 62, 22, 9, 1, 1, 30, 30, 18, 30, 30] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 379 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919427 none CC#CCC(NC(=O)C1=CC=C(OC2=CC=CC=C2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 78, 78, 30, 78, 30, 30, 30, 5, 1, 1, 1, 1, 1, 1, 1, 30, 131, 165, 165, 201, 201, 201, 201, 201, 131, 78, 30, 30, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 917 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919427 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919427 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919427/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919427 Building REAL300004919428 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919428' /scratch/stefan/7775247/working/building/REAL300004919428 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919428 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919428/0 /scratch/stefan/7775247/working/building/REAL300004919428 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/428 `/scratch/stefan/7775247/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1COCCN1C(=O)OC(C)(C)C)C(=O)[O-]) `REAL300004919428.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919428 none CC#CCC(NC(=O)C1COCCN1C(=O)OC(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 12, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 9, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 11, 11, 11, 9, 13, 13, 20, 20, 20, 20, 20, 9, 4, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11] 38 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 7, 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]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919428 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919428 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919428/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919428 Building REAL300004919429 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919429' /scratch/stefan/7775247/working/building/REAL300004919429 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919429 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919429/0 /scratch/stefan/7775247/working/building/REAL300004919429 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 429) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/429 `/scratch/stefan/7775247/working/3D/429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C)CCCN1C(=O)OC(C)(C)C)C(=O)[O-]) `REAL300004919429.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919429 none CC#CCC(NC(=O)C1(C)CCCN1C(=O)OC(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 33, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 18, 18, 18, 33, 47, 47, 82, 82, 82, 82, 82, 33, 11, 2, 2, 2, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18] 192 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 417 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919429 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919429 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919429/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919429 Building REAL300004919430 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919430' /scratch/stefan/7775247/working/building/REAL300004919430 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919430 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919430/0 /scratch/stefan/7775247/working/building/REAL300004919430 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/430 `/scratch/stefan/7775247/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1CN1C=NC=N1)C(=O)[O-]) `REAL300004919430.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919430 none CC#CCC(NC(=O)C1=CC=CC=C1CN1C=NC=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 8, 1, 8, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 20, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 6, 21, 21, 21, 21, 20, 27, 27, 40, 40, 40, 40, 40, 20, 8, 1, 1, 1, 1, 6, 6, 21, 21] 86 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919430 none CC#CCC(NC(=O)C1=CC=CC=C1CN1C=NC=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 8, 1, 8, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 59, 38, 38, 21, 38, 21, 21, 21, 21, 21, 9, 1, 1, 1, 1, 1, 1, 59, 71, 71, 86, 86, 86, 86, 86, 59, 38, 21, 21, 21, 21, 9, 9, 1, 1] 86 rigid atoms, others: [36, 37, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 398 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919430 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919430 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919430/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919430 Building REAL300004919431 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919431' /scratch/stefan/7775247/working/building/REAL300004919431 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919431 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919431/0 /scratch/stefan/7775247/working/building/REAL300004919431 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 431) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/431 `/scratch/stefan/7775247/working/3D/431' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=C(C)C=C2)CCOCC1)C(=O)[O-]) `REAL300004919431.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919431 none CC#CCC(NC(=O)C1(C2=CC=C(C)C=C2)CCOCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 5, 1, 1, 5, 5, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 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: [89, 89, 89, 24, 6, 6, 1, 6, 1, 1, 7, 7, 1, 1, 7, 7, 1, 1, 1, 1, 1, 24, 39, 39, 89, 89, 89, 89, 89, 24, 6, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1] 121 rigid atoms, others: [45, 38, 6, 39, 8, 9, 42, 43, 44, 16, 17, 18, 19, 20, 41, 40] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 424 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: REAL300004919431 none CC#CCC(NC(=O)C1(C2=CC=C(C)C=C2)CCOCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 5, 1, 1, 5, 5, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 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: [121, 121, 121, 56, 21, 21, 7, 21, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 56, 81, 81, 121, 121, 121, 121, 121, 56, 21, 1, 1, 2, 2, 2, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] 121 rigid atoms, others: [32, 36, 37, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 590 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919431 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919431 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919431/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919431 Building REAL300004919432 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919432' /scratch/stefan/7775247/working/building/REAL300004919432 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919432 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919432/0 /scratch/stefan/7775247/working/building/REAL300004919432 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/432 `/scratch/stefan/7775247/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CC)SC1=CC=CC=C1)C(=O)[O-]) `REAL300004919432.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919432 none CC#CCC(NC(=O)C(CC)SC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 5, 5, 14, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 158, 88, 50, 50, 16, 50, 7, 16, 28, 1, 1, 1, 1, 1, 1, 1, 88, 113, 113, 158, 158, 158, 158, 158, 88, 50, 16, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 813 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919432 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919432 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919432/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919432 Building REAL300004919433 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919433' /scratch/stefan/7775247/working/building/REAL300004919433 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919433 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919433/0 /scratch/stefan/7775247/working/building/REAL300004919433 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/433 `/scratch/stefan/7775247/working/3D/433' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C2=CC=CC=C2)=CC=C1Cl)C(=O)[O-]) `REAL300004919433.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919433 none CC#CCC(NC(=O)C1=CC(C2=CC=CC=C2)=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 29, 7, 7, 1, 7, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 1, 1, 29, 45, 45, 99, 99, 99, 99, 99, 29, 7, 1, 3, 3, 1, 3, 3, 1, 1] 130 rigid atoms, others: [37, 6, 8, 9, 10, 11, 17, 18, 19, 20, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 443 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919433 none CC#CCC(NC(=O)C1=CC(C2=CC=CC=C2)=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [130, 130, 130, 51, 13, 13, 3, 13, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 51, 76, 76, 130, 130, 130, 130, 130, 51, 13, 3, 1, 1, 1, 1, 1, 3, 3] 130 rigid atoms, others: [32, 33, 34, 35, 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, 37, 38]) total number of confs: 599 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919433 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919433 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919433/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919433 Building REAL300004919434 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919434' /scratch/stefan/7775247/working/building/REAL300004919434 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919434 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919434/0 /scratch/stefan/7775247/working/building/REAL300004919434 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/434 `/scratch/stefan/7775247/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(CC2=CC=CC(OC)=C2)CC2CCC1C2)C(=O)[O-]) `REAL300004919434.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919434 none CC#CCC(NC(=O)C1(CC2=CC=CC(OC)=C2)CC2CCC1C2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 12, 5, 1, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 2, 2, 2, 1, 2, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 4 rigid atoms, others: [51, 50, 6, 8, 9, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919434 none CC#CCC(NC(=O)C1(CC2=CC=CC(OC)=C2)CC2CCC1C2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 12, 5, 1, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 3, 3, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 2, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 3, 3, 2, 2, 1, 1, 1, 2, 2, 2, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 4 rigid atoms, others: [36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 19 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919434 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919434 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919434/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919434 Building REAL300004919435 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919435' /scratch/stefan/7775247/working/building/REAL300004919435 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919435 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919435/0 /scratch/stefan/7775247/working/building/REAL300004919435 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/435 `/scratch/stefan/7775247/working/3D/435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(N2CCCS2(=O)=O)C=C1C)C(=O)[O-]) `REAL300004919435.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919435 none CC#CCC(NC(=O)C1=CC=C(N2CCCS2(=O)=O)C=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 5, 14, 11, 11, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 10, 10, 1, 10, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 1, 1, 1, 25, 35, 35, 45, 45, 45, 45, 45, 25, 10, 1, 1, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 40, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 41, 42, 43]) 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: REAL300004919435 none CC#CCC(NC(=O)C1=CC=C(N2CCCS2(=O)=O)C=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 5, 14, 11, 11, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 36, 13, 13, 1, 13, 1, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 36, 49, 49, 73, 73, 73, 73, 73, 36, 13, 13, 13, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13] 201 rigid atoms, others: [34, 35, 36, 37, 39, 11, 12, 13, 14, 15, 16, 17, 18, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43]) total number of confs: 364 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919435 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919435 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919435/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919435 Building REAL300004919436 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919436' /scratch/stefan/7775247/working/building/REAL300004919436 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919436 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919436/0 /scratch/stefan/7775247/working/building/REAL300004919436 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/436 `/scratch/stefan/7775247/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(NC(=O)OC(C)(C)C)CC2=CC=CC=C2C1)C(=O)[O-]) `REAL300004919436.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919436 none CC#CCC(NC(=O)C1(NC(=O)OC(C)(C)C)CC2=CC=CC=C2C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 29, 10, 10, 1, 10, 1, 1, 4, 7, 7, 19, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 29, 42, 42, 72, 72, 72, 72, 72, 29, 10, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [51, 50, 6, 49, 8, 9, 45, 46, 47, 48, 17, 18, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 387 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919436 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919436 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919436/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919436 Building REAL300004919437 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919437' /scratch/stefan/7775247/working/building/REAL300004919437 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919437 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919437/0 /scratch/stefan/7775247/working/building/REAL300004919437 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 437) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/437 `/scratch/stefan/7775247/working/3D/437' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CSC1=NN=CN1C(C)C)C(=O)[O-]) `REAL300004919437.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919437 none CC#CCC(NC(=O)CSC1=NN=CN1C(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 8, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [195, 195, 195, 101, 70, 70, 20, 70, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 101, 143, 143, 195, 195, 195, 195, 195, 101, 70, 20, 20, 1, 3, 4, 4, 4, 4, 4, 4] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 1009 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919437 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919437 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919437/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919437 Building REAL300004919438 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919438' /scratch/stefan/7775247/working/building/REAL300004919438 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919438 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919438/0 /scratch/stefan/7775247/working/building/REAL300004919438 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/438 `/scratch/stefan/7775247/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CNN=C1C1=CC=C(F)C=C1)C(=O)[O-]) `REAL300004919438.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919438 none CC#CCC(NC(=O)C1=CNN=C1C1=CC=C(F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [161, 161, 161, 56, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 6, 1, 2, 6, 6, 56, 86, 86, 161, 161, 161, 161, 161, 56, 12, 1, 1, 6, 6, 6, 6] 200 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 760 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: REAL300004919438 none CC#CCC(NC(=O)C1=CNN=C1C1=CC=C(F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [200, 200, 200, 105, 39, 39, 6, 39, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 105, 136, 136, 200, 200, 200, 200, 200, 105, 39, 6, 6, 1, 1, 1, 1] 200 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 915 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919438 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919438 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919438/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919438 Building REAL300004919439 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919439' /scratch/stefan/7775247/working/building/REAL300004919439 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919439 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919439/0 /scratch/stefan/7775247/working/building/REAL300004919439 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 439) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/439 `/scratch/stefan/7775247/working/3D/439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCCN1C(=O)C1=CC=CC=C1)C(=O)[O-]) `REAL300004919439.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919439 none CC#CCC(NC(=O)C1CCCCN1C(=O)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 3, 4, 4, 10, 14, 14, 24, 24, 24, 24, 24, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4] 25 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45]) total number of confs: 125 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919439 none CC#CCC(NC(=O)C1CCCCN1C(=O)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 12, 6, 6, 4, 6, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 17, 17, 25, 25, 25, 25, 25, 12, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1] 25 rigid atoms, others: [41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 125 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919439 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919439 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919439/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919439 Building REAL300004919440 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919440' /scratch/stefan/7775247/working/building/REAL300004919440 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919440 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919440/0 /scratch/stefan/7775247/working/building/REAL300004919440 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/440 `/scratch/stefan/7775247/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CSC(C2=CC=CC(C(F)(F)F)=C2)=N1)C(=O)[O-]) `REAL300004919440.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919440 none CC#CCC(NC(=O)C1=CSC(C2=CC=CC(C(F)(F)F)=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 40, 11, 11, 1, 11, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 5, 5, 5, 5, 1, 40, 58, 58, 100, 100, 100, 100, 100, 40, 11, 1, 5, 5, 2, 5] 157 rigid atoms, others: [33, 6, 8, 9, 10, 11, 12, 22] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37]) total number of confs: 477 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919440 none CC#CCC(NC(=O)C1=CSC(C2=CC=CC(C(F)(F)F)=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [157, 157, 157, 97, 43, 43, 5, 43, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 97, 121, 121, 157, 157, 157, 157, 157, 97, 43, 5, 1, 1, 1, 1] 157 rigid atoms, others: [34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 732 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919440 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919440 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919440/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919440 Building REAL300004919441 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919441' /scratch/stefan/7775247/working/building/REAL300004919441 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919441 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919441/0 /scratch/stefan/7775247/working/building/REAL300004919441 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 441) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/441 `/scratch/stefan/7775247/working/3D/441' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCN(C2=CN=CC=N2)CC1)C(=O)[O-]) `REAL300004919441.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919441 none CC#CCC(NC(=O)C1CCN(C2=CN=CC=N2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 1, 8, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [130, 130, 130, 51, 13, 13, 1, 13, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1, 51, 76, 76, 130, 130, 130, 130, 130, 51, 13, 1, 1, 1, 1, 1, 8, 8, 8, 1, 1, 1, 1] 199 rigid atoms, others: [32, 33, 34, 38, 6, 39, 8, 9, 10, 11, 12, 40, 18, 19, 41, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37]) total number of confs: 609 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: REAL300004919441 none CC#CCC(NC(=O)C1CCN(C2=CN=CC=N2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 1, 8, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [199, 199, 199, 127, 65, 65, 8, 65, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 127, 153, 153, 199, 199, 199, 199, 199, 127, 65, 8, 8, 8, 8, 8, 1, 1, 1, 8, 8, 8, 8] 199 rigid atoms, others: [35, 36, 37, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41]) total number of confs: 883 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919441 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919441 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919441/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919441 Building REAL300004919442 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919442' /scratch/stefan/7775247/working/building/REAL300004919442 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004919442 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919442/0 /scratch/stefan/7775247/working/building/REAL300004919442 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/442 `/scratch/stefan/7775247/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CSC(NC(=O)C(C)C)=N1)C(=O)[O-]) `REAL300004919442.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919442 none CC#CCC(NC(=O)CC1=CSC(NC(=O)C(C)C)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 1, 1, 14, 1, 8, 1, 11, 5, 5, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [117, 117, 117, 53, 26, 26, 7, 26, 1, 1, 1, 1, 1, 1, 2, 3, 3, 13, 13, 1, 53, 80, 80, 117, 117, 117, 117, 117, 53, 26, 7, 7, 1, 2, 13, 14, 14, 14, 14, 14, 14] 201 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 665 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919442 /scratch/stefan/7775247/working /scratch/stefan/7775247 mkdir: created directory `1' /scratch/stefan/7775247/working/building/REAL300004919442/1 /scratch/stefan/7775247/working/building/REAL300004919442 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 1 (index: 443) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/443 `/scratch/stefan/7775247/working/3D/443' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CSC([N-]C(=O)C(C)C)=N1)C(=O)[O-]) `REAL300004919442.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004919442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919442/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919442 none CC#CCC(NC(=O)CC1=CSC([N-]C(=O)C(C)C)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 1, 1, 14, 1, 8, 1, 11, 5, 5, 5, 8, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 30, 17, 17, 6, 17, 1, 1, 1, 1, 1, 1, 12, 23, 23, 34, 34, 1, 30, 44, 44, 59, 59, 59, 59, 59, 30, 17, 6, 6, 1, 34, 34, 34, 34, 34, 34, 34] 201 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 427 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919442 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919442 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 1: /scratch/stefan/7775247/working/building/REAL300004919442/1.* 0: /scratch/stefan/7775247/working/building/REAL300004919442/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919442 Building REAL300004919443 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919443' /scratch/stefan/7775247/working/building/REAL300004919443 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919443 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919443/0 /scratch/stefan/7775247/working/building/REAL300004919443 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/444 `/scratch/stefan/7775247/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(OCC2=CC=CN=C2)=C1)C(=O)[O-]) `REAL300004919443.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919443 none CC#CCC(NC(=O)C1=CC=CC(OCC2=CC=CN=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 3, 3, 16, 16, 16, 16, 16, 1, 14, 26, 26, 34, 34, 34, 34, 34, 14, 5, 1, 1, 1, 3, 3, 16, 16, 16, 16, 1] 201 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 21, 41] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919443 none CC#CCC(NC(=O)C1=CC=CC(OCC2=CC=CN=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 109, 51, 51, 16, 51, 16, 15, 16, 16, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 109, 139, 139, 201, 201, 201, 201, 201, 109, 51, 15, 16, 16, 8, 8, 1, 1, 1, 1, 16] 201 rigid atoms, others: [37, 38, 39, 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, 41]) total number of confs: 944 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919443 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919443 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919443/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919443 Building REAL300004919444 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919444' /scratch/stefan/7775247/working/building/REAL300004919444 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919444 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919444/0 /scratch/stefan/7775247/working/building/REAL300004919444 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 445) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/445 `/scratch/stefan/7775247/working/3D/445' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(N2CCOCC2)C=C1)C(=O)[O-]) `REAL300004919444.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919444 none CC#CCC(NC(=O)C1=CC=C(N2CCOCC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 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: [40, 40, 40, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 1, 1, 14, 23, 23, 40, 40, 40, 40, 40, 14, 4, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1] 87 rigid atoms, others: [6, 8, 9, 10, 11, 12, 40, 18, 19, 41, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 200 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919444 none CC#CCC(NC(=O)C1=CC=C(N2CCOCC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 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: [87, 87, 87, 46, 19, 19, 1, 19, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 46, 60, 60, 87, 87, 87, 87, 87, 46, 19, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 87 rigid atoms, others: [32, 33, 34, 35, 36, 37, 39, 11, 12, 13, 14, 15, 16, 17, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41]) total number of confs: 421 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919444 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919444 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919444/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919444 Building REAL300004919445 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919445' /scratch/stefan/7775247/working/building/REAL300004919445 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919445 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919445/0 /scratch/stefan/7775247/working/building/REAL300004919445 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/446 `/scratch/stefan/7775247/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1N1CCOCC1)C(=O)[O-]) `REAL300004919445.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919445 none CC#CCC(NC(=O)C1=CC=CC=C1N1CCOCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 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: [70, 70, 70, 32, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 32, 46, 46, 70, 70, 70, 70, 70, 32, 12, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3] 74 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 333 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: REAL300004919445 none CC#CCC(NC(=O)C1=CC=CC=C1N1CCOCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 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: [74, 74, 74, 37, 18, 18, 3, 18, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 37, 50, 50, 74, 74, 74, 74, 74, 37, 18, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1] 74 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 339 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919445 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919445 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919445/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919445 Building REAL300004919446 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919446' /scratch/stefan/7775247/working/building/REAL300004919446 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919446 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919446/0 /scratch/stefan/7775247/working/building/REAL300004919446 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 447) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/447 `/scratch/stefan/7775247/working/3D/447' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C2CCCCCN2C(C2=CC=CC=C2)=N1)C(=O)[O-]) `REAL300004919446.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919446 none CC#CCC(NC(=O)C1=C2CCCCCN2C(C2=CC=CC=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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: [122, 122, 122, 38, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 38, 61, 61, 122, 122, 122, 122, 122, 38, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4] 137 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 44, 45, 46, 47, 48]) total number of confs: 577 number of broken/clashed sets: 137 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919446 none CC#CCC(NC(=O)C1=C2CCCCCN2C(C2=CC=CC=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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: [137, 137, 137, 78, 27, 27, 4, 27, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 78, 99, 99, 137, 137, 137, 137, 137, 78, 27, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1] 137 rigid atoms, others: [48, 44, 45, 46, 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]) total number of confs: 654 number of broken/clashed sets: 137 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919446 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919446 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919446/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919446 Building REAL300004919447 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919447' /scratch/stefan/7775247/working/building/REAL300004919447 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300004919447 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919447/0 /scratch/stefan/7775247/working/building/REAL300004919447 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/448 `/scratch/stefan/7775247/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCC[N@@H+]1CC1=CC=CC=C1)C(=O)[O-]) `REAL300004919447.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919447 none CC#CCC(NC(=O)C1CCC[N@@H+]1CC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [23, 23, 23, 7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 3, 4, 4, 7, 10, 10, 23, 23, 23, 23, 23, 7, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 3, 4, 4] 34 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 108 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919447 none CC#CCC(NC(=O)C1CCC[N@@H+]1CC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 12, 5, 5, 4, 5, 4, 4, 4, 4, 2, 4, 1, 1, 1, 1, 1, 1, 1, 12, 18, 18, 34, 34, 34, 34, 34, 12, 5, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 1] 34 rigid atoms, others: [40, 41, 42, 43, 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]) total number of confs: 155 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919447 /scratch/stefan/7775247/working /scratch/stefan/7775247 mkdir: created directory `1' /scratch/stefan/7775247/working/building/REAL300004919447/1 /scratch/stefan/7775247/working/building/REAL300004919447 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 1 (index: 449) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/449 `/scratch/stefan/7775247/working/3D/449' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCC[N@H+]1CC1=CC=CC=C1)C(=O)[O-]) `REAL300004919447.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004919447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919447/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919447 none CC#CCC(NC(=O)C1CCC[N@H+]1CC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 3, 4, 4, 14, 19, 19, 35, 35, 35, 35, 35, 14, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 3, 4, 4] 46 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 169 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: REAL300004919447 none CC#CCC(NC(=O)C1CCC[N@H+]1CC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 26, 10, 10, 4, 10, 4, 4, 4, 4, 2, 4, 1, 1, 1, 1, 1, 1, 1, 26, 32, 32, 46, 46, 46, 46, 46, 26, 10, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 1] 46 rigid atoms, others: [40, 41, 42, 43, 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]) total number of confs: 214 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919447 /scratch/stefan/7775247/working /scratch/stefan/7775247 mkdir: created directory `2' /scratch/stefan/7775247/working/building/REAL300004919447/2 /scratch/stefan/7775247/working/building/REAL300004919447 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 2 (index: 450) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/450 `/scratch/stefan/7775247/working/3D/450' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCN1CC1=CC=CC=C1)C(=O)[O-]) `REAL300004919447.mol2' -> `2.mol2' `temp.mol2' -> `REAL300004919447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919447/2/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: REAL300004919447 none CC#CCC(NC(=O)C1CCCN1CC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 40, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 8, 8, 6, 8, 8, 40, 65, 65, 114, 114, 114, 114, 114, 40, 12, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 8] 201 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 573 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919447 none CC#CCC(NC(=O)C1CCCN1CC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 108, 43, 43, 8, 43, 8, 8, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 108, 140, 140, 201, 201, 201, 201, 201, 108, 43, 8, 8, 8, 8, 8, 8, 8, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 43, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 959 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919447 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919447 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 2: /scratch/stefan/7775247/working/building/REAL300004919447/2.* 1: /scratch/stefan/7775247/working/building/REAL300004919447/1.* 0: /scratch/stefan/7775247/working/building/REAL300004919447/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919447 Building REAL300004919448 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919448' /scratch/stefan/7775247/working/building/REAL300004919448 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919448 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919448/0 /scratch/stefan/7775247/working/building/REAL300004919448 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 451) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/451 `/scratch/stefan/7775247/working/3D/451' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CSC(CC2=CC=C(F)C=C2)=N1)C(=O)[O-]) `REAL300004919448.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919448 none CC#CCC(NC(=O)CC1=CSC(CC2=CC=C(F)C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 1, 1, 14, 1, 5, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [52, 52, 52, 30, 16, 16, 5, 16, 1, 1, 1, 1, 1, 1, 8, 12, 12, 9, 8, 12, 12, 1, 30, 30, 30, 52, 52, 52, 52, 52, 30, 16, 5, 5, 1, 8, 8, 12, 12, 12, 12] 118 rigid atoms, others: [34, 8, 9, 10, 11, 12, 13, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 265 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919448 none CC#CCC(NC(=O)CC1=CSC(CC2=CC=C(F)C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 1, 1, 14, 1, 5, 1, 1, 1, 1, 15, 1, 1, 8, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [118, 118, 118, 107, 67, 67, 24, 67, 12, 12, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 12, 107, 107, 107, 118, 118, 118, 118, 118, 107, 67, 24, 24, 12, 4, 4, 1, 1, 1, 1] 118 rigid atoms, others: [37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 505 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919448 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919448 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919448/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919448 Building REAL300004919449 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919449' /scratch/stefan/7775247/working/building/REAL300004919449 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919449 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919449/0 /scratch/stefan/7775247/working/building/REAL300004919449 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/452 `/scratch/stefan/7775247/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(NC(=O)OC)=C1)C(=O)[O-]) `REAL300004919449.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919449 none CC#CCC(NC(=O)C1=CC=CC(NC(=O)OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 9, 14, 14, 14, 1, 13, 21, 21, 38, 38, 38, 38, 38, 13, 5, 1, 1, 1, 9, 14, 14, 14, 1] 201 rigid atoms, others: [36, 6, 8, 9, 10, 11, 12, 13, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919449 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919449 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919449/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919449 Building REAL300004919450 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919450' /scratch/stefan/7775247/working/building/REAL300004919450 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919450 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919450/0 /scratch/stefan/7775247/working/building/REAL300004919450 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 453) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/453 `/scratch/stefan/7775247/working/3D/453' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=C(CCC2)C(S(N)(=O)=O)=C1)C(=O)[O-]) `REAL300004919450.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919450 none CC#CCC(NC(=O)C1=CC2=C(CCC2)C(S(N)(=O)=O)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 1, 14, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 25, 40, 40, 78, 78, 78, 78, 78, 25, 7, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1] 166 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39]) total number of confs: 375 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919450 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919450 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919450/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919450 Building REAL300004919451 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919451' /scratch/stefan/7775247/working/building/REAL300004919451 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919451 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919451/0 /scratch/stefan/7775247/working/building/REAL300004919451 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/454 `/scratch/stefan/7775247/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(=O)C1=CN(C2=CC=CC=C2)N=C1)C(=O)[O-]) `REAL300004919451.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919451 none CC#CCC(NC(=O)C(=O)C1=CN(C2=CC=CC=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 43, 42, 9, 43, 1, 9, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 1, 116, 149, 149, 201, 201, 201, 201, 201, 116, 43, 1, 4, 4, 2, 4, 4, 1] 201 rigid atoms, others: [37, 8, 10, 11, 12, 13, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 964 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919451 none CC#CCC(NC(=O)C(=O)C1=CN(C2=CC=CC=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 123, 50, 50, 15, 50, 4, 15, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 123, 153, 153, 201, 201, 201, 201, 201, 123, 50, 4, 1, 1, 1, 1, 1, 4] 201 rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37]) total number of confs: 937 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919451 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919451 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919451/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919451 Building REAL300004919452 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919452' /scratch/stefan/7775247/working/building/REAL300004919452 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919452 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919452/0 /scratch/stefan/7775247/working/building/REAL300004919452 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 455) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/455 `/scratch/stefan/7775247/working/3D/455' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1CN1C=CC=N1)C(=O)[O-]) `REAL300004919452.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919452 none CC#CCC(NC(=O)C1=CC=CC=C1CN1C=CC=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 1, 8, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 19, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 17, 17, 17, 17, 19, 26, 26, 39, 39, 39, 39, 39, 19, 8, 1, 1, 1, 1, 5, 5, 17, 17, 17] 76 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919452 none CC#CCC(NC(=O)C1=CC=CC=C1CN1C=CC=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 1, 8, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 52, 33, 33, 17, 33, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 52, 62, 62, 76, 76, 76, 76, 76, 52, 33, 17, 17, 17, 17, 9, 9, 1, 1, 1] 76 rigid atoms, others: [36, 37, 38, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 347 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919452 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919452 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919452/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919452 Building REAL300004919453 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919453' /scratch/stefan/7775247/working/building/REAL300004919453 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919453 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919453/0 /scratch/stefan/7775247/working/building/REAL300004919453 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/456 `/scratch/stefan/7775247/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=NNC(C)=N2)C=C1)C(=O)[O-]) `REAL300004919453.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919453 none CC#CCC(NC(=O)C1=CC=C(C2=NNC(C)=N2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 1, 14, 20, 20, 37, 37, 37, 37, 37, 14, 4, 1, 1, 4, 5, 5, 5, 1, 1] 62 rigid atoms, others: [36, 37, 6, 8, 9, 10, 11, 12, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) 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: REAL300004919453 none CC#CCC(NC(=O)C1=CC=C(C2=NNC(C)=N2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 5, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 28, 11, 11, 2, 11, 2, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 28, 37, 37, 62, 62, 62, 62, 62, 28, 11, 4, 4, 1, 2, 2, 2, 4, 4] 62 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 286 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919453 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919453 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919453/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919453 Building REAL300004919454 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919454' /scratch/stefan/7775247/working/building/REAL300004919454 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919454 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919454/0 /scratch/stefan/7775247/working/building/REAL300004919454 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 457) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/457 `/scratch/stefan/7775247/working/3D/457' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(C2=CC=C(Br)C=C2)C=N1)C(=O)[O-]) `REAL300004919454.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919454 none CC#CCC(NC(=O)C1=CN(C2=CC=C(Br)C=C2)C=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [76, 76, 76, 33, 11, 11, 1, 11, 1, 1, 1, 1, 6, 6, 2, 3, 6, 6, 1, 1, 33, 48, 48, 76, 76, 76, 76, 76, 33, 11, 1, 6, 6, 6, 6, 1] 91 rigid atoms, others: [35, 6, 8, 9, 10, 11, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 373 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919454 none CC#CCC(NC(=O)C1=CN(C2=CC=C(Br)C=C2)C=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 17, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 59, 31, 31, 6, 31, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 59, 71, 71, 91, 91, 91, 91, 91, 59, 31, 6, 1, 1, 1, 1, 6] 91 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 395 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919454 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919454 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919454/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919454 Building REAL300004919455 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919455' /scratch/stefan/7775247/working/building/REAL300004919455 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919455 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919455/0 /scratch/stefan/7775247/working/building/REAL300004919455 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/458 `/scratch/stefan/7775247/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CNS(=O)(=O)CCCOC)C(=O)[O-]) `REAL300004919455.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.0.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.0.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.0.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919455 none CC#CCC(NC(=O)CNS(=O)(=O)CCCOC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 8, 14, 11, 11, 5, 5, 5, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 6, 7, 7, 7, 3, 7, 7, 2, 2, 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: [14, 14, 14, 11, 8, 8, 1, 8, 1, 1, 5, 6, 6, 6, 12, 12, 17, 18, 11, 13, 13, 14, 14, 14, 14, 14, 11, 8, 1, 1, 5, 12, 12, 12, 12, 17, 17, 18, 18, 18] 31 rigid atoms, others: [8, 9, 28, 29, 6] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 136 number of broken/clashed sets: 0 ./output.0.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919455 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919455 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919455/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919455 Building REAL300004919456 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919456' /scratch/stefan/7775247/working/building/REAL300004919456 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919456 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919456/0 /scratch/stefan/7775247/working/building/REAL300004919456 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 459) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/459 `/scratch/stefan/7775247/working/3D/459' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N=C(C2=CC=CC(C(F)(F)F)=C2)N1)C(=O)[O-]) `REAL300004919456.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919456 none CC#CCC(NC(=O)C1=C(C)N=C(C2=CC=CC(C(F)(F)F)=C2)N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 13, 13, 1, 13, 13, 13, 13, 13, 13, 1, 25, 42, 42, 64, 64, 64, 64, 64, 25, 10, 2, 2, 2, 13, 13, 1, 13, 1] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 41, 23] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 353 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: REAL300004919456 none CC#CCC(NC(=O)C1=C(C)N=C(C2=CC=CC(C(F)(F)F)=C2)N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 77, 77, 13, 77, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 140, 164, 164, 201, 201, 201, 201, 201, 140, 77, 13, 13, 13, 1, 1, 1, 1, 13] 201 rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41]) total number of confs: 907 number of broken/clashed sets: 43 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919456 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919456 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919456/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919456 Building REAL300004919457 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919457' /scratch/stefan/7775247/working/building/REAL300004919457 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919457 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919457/0 /scratch/stefan/7775247/working/building/REAL300004919457 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/460 `/scratch/stefan/7775247/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=NC(C2CCCC2)=NO1)C(=O)[O-]) `REAL300004919457.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919457 none CC#CCC(NC(=O)CCC1=NC(C2CCCC2)=NO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 1, 8, 1, 5, 5, 5, 5, 5, 8, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 74, 58, 58, 18, 57, 8, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 1, 74, 94, 94, 90, 90, 90, 90, 90, 74, 58, 19, 19, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [9, 10, 11, 12, 13, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 487 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919457 none CC#CCC(NC(=O)CCC1=NC(C2CCCC2)=NO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 1, 8, 1, 5, 5, 5, 5, 5, 8, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 156, 156, 86, 156, 59, 13, 13, 13, 1, 1, 1, 1, 1, 1, 13, 13, 179, 201, 201, 201, 201, 201, 201, 201, 179, 156, 86, 86, 59, 59, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 925 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919457 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919457 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919457/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919457 Building REAL300004919458 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919458' /scratch/stefan/7775247/working/building/REAL300004919458 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919458 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919458/0 /scratch/stefan/7775247/working/building/REAL300004919458 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 461) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/461 `/scratch/stefan/7775247/working/3D/461' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)NC)=C1)C(=O)[O-]) `REAL300004919458.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919458 none CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)NC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 1, 17, 33, 33, 69, 69, 69, 69, 69, 17, 5, 1, 1, 1, 9, 9, 9, 9, 1] 201 rigid atoms, others: [36, 6, 8, 9, 10, 11, 12, 13, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 352 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919458 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919458 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919458/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919458 Building REAL300004919459 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919459' /scratch/stefan/7775247/working/building/REAL300004919459 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919459 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919459/0 /scratch/stefan/7775247/working/building/REAL300004919459 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/462 `/scratch/stefan/7775247/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CNC(=O)C1=CC=C(C(F)(F)F)C=C1)C(=O)[O-]) `REAL300004919459.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919459 none CC#CCC(NC(=O)CNC(=O)C1=CC=C(C(F)(F)F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 124, 71, 71, 13, 71, 3, 3, 1, 3, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 124, 158, 158, 201, 201, 201, 201, 201, 124, 71, 13, 13, 3, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 10, 12, 13, 14, 15, 16, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 967 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919459 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919459 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919459/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919459 Building REAL300004919460 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919460' /scratch/stefan/7775247/working/building/REAL300004919460 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919460 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919460/0 /scratch/stefan/7775247/working/building/REAL300004919460 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 463) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/463 `/scratch/stefan/7775247/working/3D/463' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(Cl)N=C2C=CC=CN21)C(=O)[O-]) `REAL300004919460.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919460 none CC#CCC(NC(=O)C1=C(Cl)N=C2C=CC=CN21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 16, 8, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 38, 38, 60, 60, 60, 60, 60, 27, 7, 1, 1, 1, 1] 60 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919460 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919460 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919460/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919460 Building REAL300004919461 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919461' /scratch/stefan/7775247/working/building/REAL300004919461 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919461 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919461/0 /scratch/stefan/7775247/working/building/REAL300004919461 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/464 `/scratch/stefan/7775247/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CSC1=NC=CN1C1=CC=CC(Cl)=C1C)C(=O)[O-]) `REAL300004919461.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919461 none CC#CCC(NC(=O)CSC1=NC=CN1C1=CC=CC(Cl)=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 14, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 139, 109, 67, 67, 24, 67, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 109, 114, 114, 139, 139, 139, 139, 139, 109, 67, 24, 24, 1, 1, 5, 5, 5, 5, 5, 5] 201 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42]) total number of confs: 590 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919461 none CC#CCC(NC(=O)CSC1=NC=CN1C1=CC=CC(Cl)=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 14, 1, 8, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 172, 112, 112, 50, 112, 21, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 172, 179, 179, 201, 201, 201, 201, 201, 172, 112, 50, 50, 5, 5, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42]) total number of confs: 843 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919461 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919461 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919461/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919461 Building REAL300004919462 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919462' /scratch/stefan/7775247/working/building/REAL300004919462 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919462 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919462/0 /scratch/stefan/7775247/working/building/REAL300004919462 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 465) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/465 `/scratch/stefan/7775247/working/3D/465' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1S(=O)CC)C(=O)[O-]) `REAL300004919462.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919462 none CC#CCC(NC(=O)C1=CC=CC=C1S(=O)CC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o', 'O.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 110, 38, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 38, 61, 61, 110, 110, 110, 110, 110, 38, 10, 1, 1, 1, 1, 8, 8, 8, 8, 8] 190 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36]) total number of confs: 544 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919462 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919462 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919462/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919462 Building REAL300004919463 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919463' /scratch/stefan/7775247/working/building/REAL300004919463 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919463 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919463/0 /scratch/stefan/7775247/working/building/REAL300004919463 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/466 `/scratch/stefan/7775247/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C2OCC(=O)NC2=C1)C(=O)[O-]) `REAL300004919463.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919463 none CC#CCC(NC(=O)C1=CC=C2OCC(=O)NC2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 11, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 38, 38, 69, 69, 69, 69, 69, 27, 7, 1, 1, 1, 1, 1, 1] 69 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 311 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919463 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919463 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919463/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919463 Building REAL300004919464 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919464' /scratch/stefan/7775247/working/building/REAL300004919464 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919464 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919464/0 /scratch/stefan/7775247/working/building/REAL300004919464 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 467) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/467 `/scratch/stefan/7775247/working/3D/467' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(CS(C)=O)=C1)C(=O)[O-]) `REAL300004919464.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919464 none CC#CCC(NC(=O)C1=CC=CC(CS(C)=O)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.o', 'C.3', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 5, 14, 5, 11, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 13, 13, 1, 17, 25, 25, 58, 58, 58, 58, 58, 17, 5, 1, 1, 1, 5, 5, 13, 13, 13, 1] 201 rigid atoms, others: [36, 6, 8, 9, 10, 11, 12, 13, 17, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919464 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919464 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919464/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919464 Building REAL300004919465 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919465' /scratch/stefan/7775247/working/building/REAL300004919465 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919465 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919465/0 /scratch/stefan/7775247/working/building/REAL300004919465 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/468 `/scratch/stefan/7775247/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(N2C=CC=C2)C=CS1)C(=O)[O-]) `REAL300004919465.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919465 none CC#CCC(NC(=O)C1=C(N2C=CC=C2)C=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [114, 114, 114, 43, 12, 12, 1, 12, 1, 1, 1, 6, 6, 6, 6, 1, 1, 1, 43, 65, 65, 114, 114, 114, 114, 114, 43, 12, 6, 6, 6, 6, 1, 1] 137 rigid atoms, others: [32, 33, 6, 8, 9, 10, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919465 none CC#CCC(NC(=O)C1=C(N2C=CC=C2)C=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [137, 137, 137, 64, 26, 26, 6, 26, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 64, 88, 88, 137, 137, 137, 137, 137, 64, 26, 1, 1, 1, 1, 6, 6] 137 rigid atoms, others: [9, 10, 11, 12, 13, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33]) total number of confs: 643 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919465 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919465 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919465/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919465 Building REAL300004919466 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919466' /scratch/stefan/7775247/working/building/REAL300004919466 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919466 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919466/0 /scratch/stefan/7775247/working/building/REAL300004919466 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 469) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/469 `/scratch/stefan/7775247/working/3D/469' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(N2C=CC=C2)N(C)N=C1)C(=O)[O-]) `REAL300004919466.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919466 none CC#CCC(NC(=O)C1=C(N2C=CC=C2)N(C)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [172, 172, 172, 61, 11, 11, 1, 11, 1, 1, 1, 6, 6, 6, 6, 1, 1, 1, 1, 61, 93, 93, 172, 172, 172, 172, 172, 61, 11, 6, 6, 6, 6, 2, 2, 2, 1] 201 rigid atoms, others: [36, 6, 8, 9, 10, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 796 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: REAL300004919466 none CC#CCC(NC(=O)C1=C(N2C=CC=C2)N(C)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 100, 38, 38, 10, 38, 10, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 100, 137, 137, 201, 201, 201, 201, 201, 100, 38, 1, 1, 1, 1, 10, 10, 10, 10] 201 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36]) total number of confs: 936 number of broken/clashed sets: 38 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919466 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919466 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919466/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919466 Building REAL300004919467 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919467' /scratch/stefan/7775247/working/building/REAL300004919467 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919467 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919467/0 /scratch/stefan/7775247/working/building/REAL300004919467 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/470 `/scratch/stefan/7775247/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCN(C(=O)COC2=CC=CC=C2)C1)C(=O)[O-]) `REAL300004919467.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919467 none CC#CCC(NC(=O)C1CCCN(C(=O)COC2=CC=CC=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 4, 4, 11, 26, 33, 33, 26, 33, 33, 1, 22, 35, 35, 47, 47, 47, 47, 47, 22, 9, 1, 1, 1, 1, 1, 1, 1, 11, 11, 33, 33, 26, 33, 33, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 48, 40, 23, 49, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 334 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919467 none CC#CCC(NC(=O)C1CCCN(C(=O)COC2=CC=CC=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 134, 89, 89, 33, 89, 33, 33, 33, 33, 25, 9, 25, 4, 1, 1, 1, 1, 1, 1, 1, 33, 134, 162, 162, 201, 201, 201, 201, 201, 134, 89, 33, 33, 33, 33, 33, 33, 33, 9, 9, 1, 1, 1, 1, 1, 33, 33] 201 rigid atoms, others: [43, 44, 45, 46, 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, 48, 49]) total number of confs: 913 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919467 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919467 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919467/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919467 Building REAL300004919468 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919468' /scratch/stefan/7775247/working/building/REAL300004919468 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919468 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919468/0 /scratch/stefan/7775247/working/building/REAL300004919468 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 471) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/471 `/scratch/stefan/7775247/working/3D/471' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(CNC(=O)C(C)(C)C)C=C1)C(=O)[O-]) `REAL300004919468.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919468 none CC#CCC(NC(=O)C1=CC=C(CNC(=O)C(C)(C)C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 6, 32, 32, 32, 35, 35, 35, 1, 1, 9, 14, 14, 24, 24, 24, 24, 24, 9, 3, 1, 1, 6, 6, 32, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 46, 47, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919468 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919468 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919468/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919468 Building REAL300004919469 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919469' /scratch/stefan/7775247/working/building/REAL300004919469 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919469 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919469/0 /scratch/stefan/7775247/working/building/REAL300004919469 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/472 `/scratch/stefan/7775247/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(CN(C)C(=O)C(C)C)C=C1)C(=O)[O-]) `REAL300004919469.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919469 none CC#CCC(NC(=O)C1=CC=C(CN(C)C(=O)C(C)C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 5, 8, 5, 1, 11, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 8, 22, 22, 37, 37, 45, 45, 1, 1, 7, 11, 11, 21, 21, 21, 21, 21, 7, 3, 1, 1, 8, 8, 23, 23, 23, 45, 45, 45, 45, 45, 45, 45, 1, 1] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 46, 47, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 267 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919469 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919469 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919469/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919469 Building REAL300004919470 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919470' /scratch/stefan/7775247/working/building/REAL300004919470 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919470 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919470/0 /scratch/stefan/7775247/working/building/REAL300004919470 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 473) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/473 `/scratch/stefan/7775247/working/3D/473' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(NC(=O)CC(C)(C)C)=CC=C1Cl)C(=O)[O-]) `REAL300004919470.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919470 none CC#CCC(NC(=O)C1=CC(NC(=O)CC(C)(C)C)=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 7, 7, 1, 7, 1, 1, 1, 1, 7, 7, 7, 17, 20, 20, 20, 1, 1, 1, 1, 20, 30, 30, 47, 47, 47, 47, 47, 20, 7, 1, 7, 17, 17, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1] 201 rigid atoms, others: [33, 6, 8, 9, 10, 11, 46, 47, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 306 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919470 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919470 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919470/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919470 Building REAL300004919471 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919471' /scratch/stefan/7775247/working/building/REAL300004919471 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919471 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919471/0 /scratch/stefan/7775247/working/building/REAL300004919471 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/474 `/scratch/stefan/7775247/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(NC(=O)CC(C)C)C(F)=C1)C(=O)[O-]) `REAL300004919471.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919471 none CC#CCC(NC(=O)C1=CC=C(NC(=O)CC(C)C)C(F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 6, 6, 6, 16, 17, 19, 1, 1, 1, 14, 22, 22, 39, 39, 39, 39, 39, 14, 5, 1, 1, 6, 16, 16, 19, 19, 19, 19, 19, 19, 19, 1] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 44, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919471 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919471 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919471/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919471 Building REAL300004919472 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919472' /scratch/stefan/7775247/working/building/REAL300004919472 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919472 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919472/0 /scratch/stefan/7775247/working/building/REAL300004919472 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 475) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/475 `/scratch/stefan/7775247/working/3D/475' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC2=CC=CC(Cl)=C2Cl)N=C1)C(=O)[O-]) `REAL300004919472.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919472 none CC#CCC(NC(=O)C1=CC=C(OC2=CC=CC(Cl)=C2Cl)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 16, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 8, 19, 19, 19, 19, 19, 19, 19, 1, 1, 15, 24, 24, 39, 39, 39, 39, 39, 15, 5, 1, 1, 19, 19, 19, 1] 201 rigid atoms, others: [33, 34, 38, 6, 8, 9, 10, 11, 12, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919472 none CC#CCC(NC(=O)C1=CC=C(OC2=CC=CC(Cl)=C2Cl)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 16, 1, 16, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 112, 55, 55, 19, 55, 19, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 112, 147, 147, 201, 201, 201, 201, 201, 112, 55, 19, 19, 1, 1, 1, 19] 201 rigid atoms, others: [35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38]) total number of confs: 947 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919472 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919472 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919472/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919472 Building REAL300004919473 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919473' /scratch/stefan/7775247/working/building/REAL300004919473 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919473 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919473/0 /scratch/stefan/7775247/working/building/REAL300004919473 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/476 `/scratch/stefan/7775247/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC)C(N2CCNC2=O)=C1)C(=O)[O-]) `REAL300004919473.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919473 none CC#CCC(NC(=O)C1=CC=C(OC)C(N2CCNC2=O)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 8, 5, 5, 8, 1, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 5, 5, 1, 5, 1, 1, 1, 1, 1, 3, 1, 1, 8, 8, 8, 8, 8, 1, 16, 29, 29, 64, 64, 64, 64, 64, 16, 5, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 1] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 14, 15, 21, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 311 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919473 none CC#CCC(NC(=O)C1=CC=C(OC)C(N2CCNC2=O)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 8, 5, 5, 8, 1, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [174, 174, 174, 75, 27, 27, 8, 27, 8, 8, 8, 8, 8, 13, 1, 1, 1, 1, 1, 1, 1, 8, 75, 119, 119, 174, 174, 174, 174, 174, 75, 27, 8, 8, 13, 13, 13, 1, 1, 1, 1, 1, 8] 201 rigid atoms, others: [37, 38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42]) total number of confs: 883 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919473 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919473 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919473/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919473 Building REAL300004919474 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919474' /scratch/stefan/7775247/working/building/REAL300004919474 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919474 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919474/0 /scratch/stefan/7775247/working/building/REAL300004919474 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 477) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/477 `/scratch/stefan/7775247/working/3D/477' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN=C(C2CCCO2)S1)C(=O)[O-]) `REAL300004919474.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919474 none CC#CCC(NC(=O)C1=CN=C(C2CCCO2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 5, 12, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 36, 12, 12, 1, 12, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 36, 56, 56, 92, 92, 92, 92, 92, 36, 12, 1, 13, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 17, 28] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 458 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919474 none CC#CCC(NC(=O)C1=CN=C(C2CCCO2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 5, 12, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 134, 71, 71, 13, 71, 13, 13, 13, 1, 1, 1, 1, 1, 1, 13, 134, 159, 159, 201, 201, 201, 201, 201, 134, 71, 13, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 871 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919474 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919474 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919474/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919474 Building REAL300004919475 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919475' /scratch/stefan/7775247/working/building/REAL300004919475 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919475 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919475/0 /scratch/stefan/7775247/working/building/REAL300004919475 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/478 `/scratch/stefan/7775247/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(CNS(C)(=O)=O)O1)C(=O)[O-]) `REAL300004919475.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919475 none CC#CCC(NC(=O)C1=CC=C(CNS(C)(=O)=O)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 8, 14, 5, 11, 11, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 5, 6, 1, 6, 1, 1, 1, 1, 1, 7, 38, 56, 56, 56, 1, 14, 22, 22, 32, 32, 32, 32, 32, 14, 6, 1, 1, 7, 7, 38, 56, 56, 56] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 368 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919475 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919475 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919475/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919475 Building REAL300004919476 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919476' /scratch/stefan/7775247/working/building/REAL300004919476 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919476 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919476/0 /scratch/stefan/7775247/working/building/REAL300004919476 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 479) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/479 `/scratch/stefan/7775247/working/3D/479' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C2C=NN(C)C2=NC(C)=C1)C(=O)[O-]) `REAL300004919476.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919476 none CC#CCC(NC(=O)C1=C2C=NN(C)C2=NC(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 1, 8, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 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: [87, 87, 87, 31, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 47, 47, 87, 87, 87, 87, 87, 31, 11, 1, 2, 2, 2, 2, 2, 2, 1] 87 rigid atoms, others: [36, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 423 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919476 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919476 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919476/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919476 Building REAL300004919477 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919477' /scratch/stefan/7775247/working/building/REAL300004919477 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919477 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919477/0 /scratch/stefan/7775247/working/building/REAL300004919477 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/480 `/scratch/stefan/7775247/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCC1=CC2=CC=CC=C2C=C1)C(=O)[O-]) `REAL300004919477.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919477 none CC#CCC(NC(=O)CCCC1=CC2=CC=CC=C2C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 133, 105, 52, 52, 10, 52, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 105, 109, 109, 133, 133, 133, 133, 133, 105, 52, 10, 10, 6, 6, 2, 2, 1, 1, 1, 1, 1, 1, 1] 133 rigid atoms, others: [43, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 592 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919477 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919477 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919477/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919477 Building REAL300004919478 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919478' /scratch/stefan/7775247/working/building/REAL300004919478 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919478 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919478/0 /scratch/stefan/7775247/working/building/REAL300004919478 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 481) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/481 `/scratch/stefan/7775247/working/3D/481' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(SC2=CC=C(Cl)C=C2)O1)C(=O)[O-]) `REAL300004919478.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919478 none CC#CCC(NC(=O)C1=CC=C(SC2=CC=C(Cl)C=C2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 1, 16, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 5, 6, 1, 6, 1, 1, 1, 1, 1, 13, 32, 32, 13, 13, 32, 32, 1, 13, 23, 23, 39, 39, 39, 39, 39, 13, 6, 1, 1, 32, 32, 32, 32] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36]) total number of confs: 276 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919478 none CC#CCC(NC(=O)C1=CC=C(SC2=CC=C(Cl)C=C2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 1, 16, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 117, 67, 67, 32, 67, 32, 32, 32, 6, 1, 1, 1, 1, 1, 1, 1, 1, 32, 117, 157, 157, 201, 201, 201, 201, 201, 117, 67, 32, 32, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 949 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919478 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919478 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919478/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919478 Building REAL300004919479 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919479' /scratch/stefan/7775247/working/building/REAL300004919479 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919479 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919479/0 /scratch/stefan/7775247/working/building/REAL300004919479 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/482 `/scratch/stefan/7775247/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC(C)CC1=CC=C(Cl)C=C1)C(=O)[O-]) `REAL300004919479.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919479 none CC#CCC(NC(=O)CC(C)CC1=CC=C(Cl)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [85, 85, 85, 70, 43, 43, 13, 43, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 70, 72, 72, 85, 85, 85, 85, 85, 70, 43, 13, 13, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1] 85 rigid atoms, others: [35, 36, 37, 38, 39, 40, 9, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 367 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919479 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919479 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919479/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919479 Building REAL300004919480 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919480' /scratch/stefan/7775247/working/building/REAL300004919480 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919480 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919480/0 /scratch/stefan/7775247/working/building/REAL300004919480 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 483) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/483 `/scratch/stefan/7775247/working/3D/483' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C(=O)NC(C)C)C=C1)C(=O)[O-]) `REAL300004919480.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919480 none CC#CCC(NC(=O)C1=CC=C(C(=O)NC(C)C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 7, 7, 7, 28, 28, 1, 1, 15, 25, 25, 57, 57, 57, 57, 57, 15, 4, 1, 1, 7, 28, 28, 28, 28, 28, 28, 28, 1, 1] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 40, 18, 19, 41, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 339 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919480 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919480 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919480/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919480 Building REAL300004919481 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919481' /scratch/stefan/7775247/working/building/REAL300004919481 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919481 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919481/0 /scratch/stefan/7775247/working/building/REAL300004919481 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/484 `/scratch/stefan/7775247/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C)=C(Br)C=C1C)C(=O)[O-]) `REAL300004919481.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919481 none CC#CCC(NC(=O)C1=CC(C)=C(Br)C=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 5, 1, 17, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [74, 74, 74, 39, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 50, 50, 74, 74, 74, 74, 74, 39, 10, 1, 2, 2, 2, 1, 2, 2, 2] 74 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 31] set([0, 1, 2, 3, 4, 5, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34]) total number of confs: 356 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919481 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919481 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919481/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919481 Building REAL300004919482 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919482' /scratch/stefan/7775247/working/building/REAL300004919482 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919482 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919482/0 /scratch/stefan/7775247/working/building/REAL300004919482 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 485) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/485 `/scratch/stefan/7775247/working/3D/485' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN=C2SC=C(C)N2C1=O)C(=O)[O-]) `REAL300004919482.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919482 none CC#CCC(NC(=O)C1=CN=C2SC=C(C)N2C1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 14, 1, 1, 5, 8, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 2, 2, 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: [85, 85, 85, 43, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 59, 59, 85, 85, 85, 85, 85, 43, 13, 1, 1, 2, 2, 2] 85 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 32, 33, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 412 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919482 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919482 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919482/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919482 Building REAL300004919483 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919483' /scratch/stefan/7775247/working/building/REAL300004919483 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919483 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919483/0 /scratch/stefan/7775247/working/building/REAL300004919483 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/486 `/scratch/stefan/7775247/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=C(Br)C(F)=C1)C(=O)[O-]) `REAL300004919483.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919483 none CC#CCC(NC(=O)CC1=CC=C(Br)C(F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 17, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 66, 18, 18, 8, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 66, 110, 110, 201, 201, 201, 201, 201, 66, 18, 8, 8, 1, 1, 1] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 992 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919483 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919483 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919483/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919483 Building REAL300004919484 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919484' /scratch/stefan/7775247/working/building/REAL300004919484 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919484 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919484/0 /scratch/stefan/7775247/working/building/REAL300004919484 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 487) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/487 `/scratch/stefan/7775247/working/3D/487' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=CC2=CC=C(OC)C=C21)C(=O)[O-]) `REAL300004919484.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919484 none CC#CCC(NC(=O)CC1=CC=CC2=CC=C(OC)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [168, 168, 168, 77, 35, 35, 6, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 77, 116, 116, 168, 168, 168, 168, 168, 77, 35, 6, 6, 1, 1, 1, 1, 1, 3, 3, 3, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40]) total number of confs: 851 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919484 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919484 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919484/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919484 Building REAL300004919485 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919485' /scratch/stefan/7775247/working/building/REAL300004919485 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919485 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919485/0 /scratch/stefan/7775247/working/building/REAL300004919485 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/488 `/scratch/stefan/7775247/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1OC1=CC=CN=C1)C(=O)[O-]) `REAL300004919485.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919485 none CC#CCC(NC(=O)C1=CC=CC=C1OC1=CC=CN=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 20, 20, 20, 20, 20, 28, 44, 44, 64, 64, 64, 64, 64, 28, 12, 1, 1, 1, 1, 20, 20, 20, 20] 201 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 348 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919485 none CC#CCC(NC(=O)C1=CC=CC=C1OC1=CC=CN=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 108, 71, 71, 20, 71, 20, 20, 20, 20, 20, 9, 1, 1, 1, 1, 1, 1, 1, 108, 154, 154, 201, 201, 201, 201, 201, 108, 71, 20, 20, 20, 20, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 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]) total number of confs: 1003 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919485 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919485 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919485/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919485 Building REAL300004919486 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919486' /scratch/stefan/7775247/working/building/REAL300004919486 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919486 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919486/0 /scratch/stefan/7775247/working/building/REAL300004919486 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 489) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/489 `/scratch/stefan/7775247/working/3D/489' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCNC(=O)C1CCCCC1)C(=O)[O-]) `REAL300004919486.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919486 none CC#CCC(NC(=O)CCNC(=O)C1CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 159, 129, 129, 61, 130, 41, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 161, 194, 194, 201, 201, 201, 199, 201, 161, 130, 61, 61, 41, 41, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 1028 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919486 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919486 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919486/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919486 Building REAL300004919487 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919487' /scratch/stefan/7775247/working/building/REAL300004919487 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919487 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919487/0 /scratch/stefan/7775247/working/building/REAL300004919487 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/490 `/scratch/stefan/7775247/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN=C2C(=C1)C=NN2CC(C)C)C(=O)[O-]) `REAL300004919487.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919487 none CC#CCC(NC(=O)C1=CN=C2C(=C1)C=NN2CC(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 8, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 7, 7, 17, 32, 32, 70, 70, 70, 70, 70, 17, 5, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 350 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919487 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919487 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919487/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919487 Building REAL300004919488 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919488' /scratch/stefan/7775247/working/building/REAL300004919488 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919488 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919488/0 /scratch/stefan/7775247/working/building/REAL300004919488 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 491) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/491 `/scratch/stefan/7775247/working/3D/491' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=NC(OC2=CC=CC=C2)=C1)C(=O)[O-]) `REAL300004919488.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919488 none CC#CCC(NC(=O)C1=CC=NC(OC2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 14, 14, 9, 14, 14, 1, 13, 21, 21, 38, 38, 38, 38, 38, 13, 5, 1, 1, 14, 14, 10, 14, 14, 1] 201 rigid atoms, others: [32, 38, 6, 8, 9, 10, 11, 12, 13, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) 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: REAL300004919488 none CC#CCC(NC(=O)C1=CC=NC(OC2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 112, 48, 48, 14, 48, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 14, 112, 142, 142, 201, 201, 201, 201, 201, 112, 48, 14, 14, 1, 1, 1, 1, 1, 14] 201 rigid atoms, others: [33, 34, 35, 36, 37, 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, 38]) total number of confs: 939 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919488 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919488 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919488/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919488 Building REAL300004919489 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919489' /scratch/stefan/7775247/working/building/REAL300004919489 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919489 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919489/0 /scratch/stefan/7775247/working/building/REAL300004919489 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/492 `/scratch/stefan/7775247/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(OC2=CC=CN=C2)C(F)=C1)C(=O)[O-]) `REAL300004919489.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919489 none CC#CCC(NC(=O)C=CC1=CC=C(OC2=CC=CN=C2)C(F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 1, 15, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 22, 22, 5, 22, 5, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 13, 13, 1, 1, 1, 31, 31, 31, 34, 34, 34, 34, 34, 31, 22, 5, 5, 1, 1, 13, 13, 13, 13, 1] 201 rigid atoms, others: [36, 37, 9, 10, 11, 12, 13, 14, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 144 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: REAL300004919489 none CC#CCC(NC(=O)C=CC1=CC=C(OC2=CC=CN=C2)C(F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 1, 15, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 146, 146, 49, 146, 49, 13, 13, 13, 13, 7, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 201, 201, 201, 201, 201, 201, 201, 201, 201, 146, 49, 49, 13, 13, 1, 1, 1, 1, 13] 201 rigid atoms, others: [38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42]) total number of confs: 718 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919489 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919489 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919489/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919489 Building REAL300004919490 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919490' /scratch/stefan/7775247/working/building/REAL300004919490 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919490 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919490/0 /scratch/stefan/7775247/working/building/REAL300004919490 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 493) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/493 `/scratch/stefan/7775247/working/3D/493' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(C2=CC=C(C(F)(F)F)C=N2)N=N1)C(=O)[O-]) `REAL300004919490.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919490 none CC#CCC(NC(=O)C1=CN(C2=CC=C(C(F)(F)F)C=N2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 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: [72, 72, 72, 34, 12, 12, 1, 12, 1, 1, 1, 1, 5, 5, 4, 4, 5, 5, 5, 5, 5, 1, 1, 34, 49, 49, 72, 72, 72, 72, 72, 34, 13, 1, 5, 5, 5] 89 rigid atoms, others: [33, 6, 8, 9, 10, 11, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36]) total number of confs: 365 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919490 none CC#CCC(NC(=O)C1=CN(C2=CC=C(C(F)(F)F)C=N2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 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, 53, 24, 24, 5, 24, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 5, 5, 53, 69, 69, 89, 89, 89, 89, 89, 53, 24, 5, 1, 1, 1] 89 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 425 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919490 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919490 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919490/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919490 Building REAL300004919491 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919491' /scratch/stefan/7775247/working/building/REAL300004919491 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919491 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919491/0 /scratch/stefan/7775247/working/building/REAL300004919491 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/494 `/scratch/stefan/7775247/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CSC=C2)N=C1C)C(=O)[O-]) `REAL300004919491.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919491 none CC#CCC(NC(=O)C1=CC=C(C2=CSC=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 10, 10, 1, 10, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 1, 1, 32, 54, 54, 79, 79, 79, 79, 79, 32, 10, 1, 1, 13, 13, 13, 2, 2, 2] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 419 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919491 none CC#CCC(NC(=O)C1=CC=C(C2=CSC=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 129, 72, 72, 12, 72, 12, 13, 13, 1, 1, 1, 1, 1, 1, 13, 13, 13, 129, 151, 151, 201, 201, 201, 201, 201, 129, 72, 13, 13, 1, 1, 1, 13, 13, 13] 201 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 876 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919491 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919491 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919491/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919491 Building REAL300004919492 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919492' /scratch/stefan/7775247/working/building/REAL300004919492 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919492 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919492/0 /scratch/stefan/7775247/working/building/REAL300004919492 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 495) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/495 `/scratch/stefan/7775247/working/3D/495' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CC=CO2)N=C1C)C(=O)[O-]) `REAL300004919492.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919492 none CC#CCC(NC(=O)C1=CC=C(C2=CC=CO2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 34, 10, 10, 1, 10, 1, 1, 1, 1, 1, 12, 12, 12, 12, 1, 1, 1, 34, 55, 55, 99, 99, 99, 99, 99, 34, 10, 1, 1, 13, 12, 12, 2, 2, 2] 168 rigid atoms, others: [6, 8, 9, 10, 11, 12, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 488 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919492 none CC#CCC(NC(=O)C1=CC=C(C2=CC=CO2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [168, 168, 168, 110, 62, 62, 12, 62, 12, 12, 12, 1, 1, 1, 1, 1, 1, 12, 12, 13, 110, 127, 127, 168, 168, 168, 168, 168, 110, 62, 12, 13, 1, 1, 1, 13, 13, 13] 168 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 722 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919492 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919492 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919492/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919492 Building REAL300004919493 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919493' /scratch/stefan/7775247/working/building/REAL300004919493 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919493 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919493/0 /scratch/stefan/7775247/working/building/REAL300004919493 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/496 `/scratch/stefan/7775247/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CNC(=O)C1=CC2=C(CCC2)S1)C(=O)[O-]) `REAL300004919493.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919493 none CC#CCC(NC(=O)CNC(=O)C1=CC2=C(CCC2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 135, 83, 84, 25, 84, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 135, 167, 167, 201, 201, 201, 201, 201, 135, 84, 25, 25, 7, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 10, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 977 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919493 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919493 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919493/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919493 Building REAL300004919494 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919494' /scratch/stefan/7775247/working/building/REAL300004919494 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919494 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919494/0 /scratch/stefan/7775247/working/building/REAL300004919494 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 497) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/497 `/scratch/stefan/7775247/working/3D/497' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C(=O)N(C)C)C=C1)C(=O)[O-]) `REAL300004919494.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919494 none CC#CCC(NC(=O)C1=CC=C(C(=O)N(C)C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 7, 7, 11, 11, 1, 1, 13, 21, 21, 41, 41, 41, 41, 41, 13, 4, 1, 1, 11, 11, 11, 11, 11, 11, 1, 1] 79 rigid atoms, others: [37, 6, 8, 9, 10, 11, 12, 17, 18, 38, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 216 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919494 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919494 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919494/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919494 Building REAL300004919495 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919495' /scratch/stefan/7775247/working/building/REAL300004919495 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919495 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919495/0 /scratch/stefan/7775247/working/building/REAL300004919495 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/498 `/scratch/stefan/7775247/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(C(=O)N(C)C)=C1)C(=O)[O-]) `REAL300004919495.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919495 none CC#CCC(NC(=O)C1=CC=CC(C(=O)N(C)C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 16, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 9, 9, 1, 16, 29, 29, 53, 53, 53, 53, 53, 16, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 1] 155 rigid atoms, others: [38, 6, 8, 9, 10, 11, 12, 13, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 277 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919495 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919495 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919495/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919495 Building REAL300004919496 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919496' /scratch/stefan/7775247/working/building/REAL300004919496 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919496 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919496/0 /scratch/stefan/7775247/working/building/REAL300004919496 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 499) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/499 `/scratch/stefan/7775247/working/3D/499' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(CN2C3=CC=CC=C3CC2C)C=CO1)C(=O)[O-]) `REAL300004919496.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919496 none CC#CCC(NC(=O)C1=C(CN2C3=CC=CC=C3CC2C)C=CO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 12, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 16, 5, 5, 1, 5, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 16, 23, 23, 35, 35, 35, 35, 35, 16, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1] 62 rigid atoms, others: [6, 8, 9, 10, 46, 47, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 193 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: REAL300004919496 none CC#CCC(NC(=O)C1=C(CN2C3=CC=CC=C3CC2C)C=CO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 12, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 37, 17, 17, 7, 17, 7, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 37, 45, 45, 62, 62, 62, 62, 62, 37, 17, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7] 62 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46, 47]) total number of confs: 301 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919496 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919496 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919496/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919496 Building REAL300004919497 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919497' /scratch/stefan/7775247/working/building/REAL300004919497 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919497 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919497/0 /scratch/stefan/7775247/working/building/REAL300004919497 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/500 `/scratch/stefan/7775247/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(CN2C3=CC=CC=C3CC2C)OC=C1)C(=O)[O-]) `REAL300004919497.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919497 none CC#CCC(NC(=O)C1=C(CN2C3=CC=CC=C3CC2C)OC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 25, 9, 9, 1, 9, 1, 1, 1, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 25, 39, 39, 59, 59, 59, 59, 59, 25, 10, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1] 201 rigid atoms, others: [6, 8, 9, 10, 46, 47, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 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: REAL300004919497 none CC#CCC(NC(=O)C1=C(CN2C3=CC=CC=C3CC2C)OC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 125, 61, 61, 19, 61, 19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 125, 163, 163, 201, 201, 201, 201, 201, 125, 61, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 19, 19] 201 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46, 47]) total number of confs: 1003 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919497 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919497 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919497/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919497 Building REAL300004919498 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919498' /scratch/stefan/7775247/working/building/REAL300004919498 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919498 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919498/0 /scratch/stefan/7775247/working/building/REAL300004919498 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 501) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/501 `/scratch/stefan/7775247/working/3D/501' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CSC(C2=CN=CC=N2)=N1)C(=O)[O-]) `REAL300004919498.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919498 none CC#CCC(NC(=O)C1=CSC(C2=CN=CC=N2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 8, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 2, 2, 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: [85, 85, 85, 35, 12, 13, 1, 13, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 1, 35, 53, 53, 85, 85, 85, 85, 85, 35, 13, 1, 12, 12, 12] 152 rigid atoms, others: [6, 8, 9, 10, 11, 12, 18, 29] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 409 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919498 none CC#CCC(NC(=O)C1=CSC(C2=CN=CC=N2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 8, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [152, 152, 152, 99, 49, 49, 12, 49, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 12, 99, 123, 123, 152, 152, 152, 152, 152, 99, 49, 12, 1, 1, 1] 152 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 700 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919498 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919498 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919498/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919498 Building REAL300004919499 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919499' /scratch/stefan/7775247/working/building/REAL300004919499 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919499 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919499/0 /scratch/stefan/7775247/working/building/REAL300004919499 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/502 `/scratch/stefan/7775247/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OCC(F)(F)C(F)F)N=C1)C(=O)[O-]) `REAL300004919499.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919499 none CC#CCC(NC(=O)C1=CC=C(OCC(F)(F)C(F)F)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 15, 15, 5, 15, 15, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 3, 14, 37, 37, 36, 47, 47, 1, 1, 13, 20, 20, 31, 31, 31, 31, 31, 13, 5, 1, 1, 14, 14, 46, 1] 201 rigid atoms, others: [32, 33, 37, 6, 8, 9, 10, 11, 12, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919499 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919499 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919499/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919499 Building REAL300004919500 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919500' /scratch/stefan/7775247/working/building/REAL300004919500 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919500 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919500/0 /scratch/stefan/7775247/working/building/REAL300004919500 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 503) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/503 `/scratch/stefan/7775247/working/3D/503' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C2CC2)=NC2=C(C)C=C(C)C=C12)C(=O)[O-]) `REAL300004919500.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919500 none CC#CCC(NC(=O)C1=CC(C2CC2)=NC2=C(C)C=C(C)C=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 1, 1, 5, 1, 1, 5, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 34, 9, 9, 1, 9, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 58, 58, 112, 112, 112, 112, 112, 34, 9, 1, 11, 11, 11, 11, 11, 2, 2, 2, 1, 2, 2, 2, 1] 201 rigid atoms, others: [33, 6, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46, 42] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 560 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919500 none CC#CCC(NC(=O)C1=CC(C2CC2)=NC2=C(C)C=C(C)C=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 1, 1, 5, 1, 1, 5, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 126, 68, 68, 11, 68, 11, 11, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 126, 153, 153, 201, 201, 201, 201, 201, 126, 68, 11, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [34, 35, 36, 37, 38, 10, 11, 12, 13] 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, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 911 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919500 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919500 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919500/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919500 Building REAL300004919501 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919501' /scratch/stefan/7775247/working/building/REAL300004919501 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919501 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919501/0 /scratch/stefan/7775247/working/building/REAL300004919501 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/504 `/scratch/stefan/7775247/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C2CC2)=NC2=CC=C(Cl)C=C21)C(=O)[O-]) `REAL300004919501.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919501 none CC#CCC(NC(=O)C1=CC(C2CC2)=NC2=CC=C(Cl)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 31, 9, 9, 1, 9, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 31, 53, 53, 99, 99, 99, 99, 99, 31, 9, 1, 11, 11, 11, 11, 11, 1, 1, 1] 201 rigid atoms, others: [32, 38, 6, 39, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 40] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 489 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919501 none CC#CCC(NC(=O)C1=CC(C2CC2)=NC2=CC=C(Cl)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 123, 65, 65, 11, 65, 11, 11, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 123, 154, 154, 201, 201, 201, 201, 201, 123, 65, 11, 1, 1, 1, 1, 1, 11, 11, 11] 201 rigid atoms, others: [33, 34, 35, 36, 37, 10, 11, 12, 13] 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, 38, 39, 40]) total number of confs: 933 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919501 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919501 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919501/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919501 Building REAL300004919502 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919502' /scratch/stefan/7775247/working/building/REAL300004919502 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919502 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919502/0 /scratch/stefan/7775247/working/building/REAL300004919502 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 505) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/505 `/scratch/stefan/7775247/working/3D/505' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(S(=O)(=O)NC)=CS1)C(=O)[O-]) `REAL300004919502.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919502 none CC#CCC(NC(=O)C1=CC(S(=O)(=O)NC)=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 35, 11, 11, 1, 11, 1, 1, 1, 1, 2, 2, 2, 13, 1, 1, 35, 52, 52, 94, 94, 94, 94, 94, 35, 11, 1, 13, 13, 13, 13, 1] 201 rigid atoms, others: [33, 6, 8, 9, 10, 11, 16, 17, 28] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 459 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919502 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919502 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919502/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919502 Building REAL300004919503 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919503' /scratch/stefan/7775247/working/building/REAL300004919503 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919503 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919503/0 /scratch/stefan/7775247/working/building/REAL300004919503 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/506 `/scratch/stefan/7775247/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC([N+](=O)[O-])=CC=C1SC(C)C)C(=O)[O-]) `REAL300004919503.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919503 none CC#CCC(NC(=O)C1=CC([N+](=O)[O-])=CC=C1SC(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 8, 11, 11, 1, 1, 1, 14, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 31, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 20, 20, 31, 48, 48, 81, 81, 81, 81, 81, 31, 11, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 441 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919503 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919503 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919503/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919503 Building REAL300004919504 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919504' /scratch/stefan/7775247/working/building/REAL300004919504 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919504 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919504/0 /scratch/stefan/7775247/working/building/REAL300004919504 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 507) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/507 `/scratch/stefan/7775247/working/3D/507' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CC=C(Br)S2)S1)C(=O)[O-]) `REAL300004919504.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919504 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(Br)S2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 17, 14, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 37, 13, 13, 1, 13, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 1, 37, 60, 60, 103, 103, 103, 103, 103, 37, 13, 1, 1, 12, 12] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32]) total number of confs: 497 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919504 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(Br)S2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 17, 14, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 12, 81, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 12, 138, 162, 162, 201, 201, 201, 201, 201, 138, 81, 12, 12, 1, 1] 201 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 862 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919504 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919504 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919504/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919504 Building REAL300004919505 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919505' /scratch/stefan/7775247/working/building/REAL300004919505 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919505 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919505/0 /scratch/stefan/7775247/working/building/REAL300004919505 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/508 `/scratch/stefan/7775247/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(OC2=CC=C(Cl)C=C2)=C1)C(=O)[O-]) `REAL300004919505.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919505 none CC#CCC(NC(=O)C1=CC=CC(OC2=CC=C(Cl)C=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 9, 16, 16, 16, 16, 16, 16, 1, 14, 20, 20, 31, 31, 31, 31, 31, 14, 5, 1, 1, 1, 16, 16, 16, 16, 1] 201 rigid atoms, others: [32, 33, 34, 6, 39, 8, 9, 10, 11, 12, 13, 21] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919505 none CC#CCC(NC(=O)C1=CC=CC(OC2=CC=C(Cl)C=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 107, 47, 47, 16, 47, 16, 16, 16, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 16, 107, 139, 139, 201, 201, 201, 201, 201, 107, 47, 16, 16, 16, 1, 1, 1, 1, 16] 201 rigid atoms, others: [35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39]) total number of confs: 917 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919505 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919505 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919505/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919505 Building REAL300004919506 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919506' /scratch/stefan/7775247/working/building/REAL300004919506 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919506 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919506/0 /scratch/stefan/7775247/working/building/REAL300004919506 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 509) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/509 `/scratch/stefan/7775247/working/3D/509' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN=CC(C2=CC=C(OC)C=C2)=C1)C(=O)[O-]) `REAL300004919506.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919506 none CC#CCC(NC(=O)C1=CN=CC(C2=CC=C(OC)C=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 19, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 5, 3, 3, 1, 19, 35, 35, 77, 77, 77, 77, 77, 19, 6, 1, 1, 3, 3, 5, 5, 5, 3, 3, 1] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 21, 41] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 362 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919506 none CC#CCC(NC(=O)C1=CN=CC(C2=CC=C(OC)C=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 139, 35, 10, 10, 3, 10, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 1, 1, 3, 35, 66, 66, 139, 139, 139, 139, 139, 35, 10, 3, 3, 1, 1, 3, 3, 3, 1, 1, 3] 201 rigid atoms, others: [34, 35, 39, 40, 12, 13, 14, 15, 16, 17, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 41]) total number of confs: 652 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919506 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919506 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919506/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919506 Building REAL300004919507 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919507' /scratch/stefan/7775247/working/building/REAL300004919507 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919507 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919507/0 /scratch/stefan/7775247/working/building/REAL300004919507 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/510 `/scratch/stefan/7775247/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN=CC(C2=CC=CC(C)=C2)=C1)C(=O)[O-]) `REAL300004919507.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919507 none CC#CCC(NC(=O)C1=CN=CC(C2=CC=CC(C)=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 3, 5, 5, 5, 1, 17, 25, 25, 60, 60, 60, 60, 60, 17, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 40, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) 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: REAL300004919507 none CC#CCC(NC(=O)C1=CN=CC(C2=CC=CC(C)=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 63, 17, 17, 5, 17, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 63, 93, 93, 201, 201, 201, 201, 201, 63, 17, 5, 5, 1, 1, 1, 2, 2, 2, 1, 5] 201 rigid atoms, others: [33, 34, 35, 39, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 40]) total number of confs: 926 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919507 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919507 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919507/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919507 Building REAL300004919508 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919508' /scratch/stefan/7775247/working/building/REAL300004919508 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919508 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919508/0 /scratch/stefan/7775247/working/building/REAL300004919508 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 511) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/511 `/scratch/stefan/7775247/working/3D/511' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NC=C(Br)C=C1Br)C(=O)[O-]) `REAL300004919508.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919508 none CC#CCC(NC(=O)C1=NC=C(Br)C=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 1, 1, 17, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 23, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 23, 33, 33, 53, 53, 53, 53, 53, 23, 7, 1, 1] 53 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919508 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919508 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919508/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919508 Building REAL300004919509 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919509' /scratch/stefan/7775247/working/building/REAL300004919509 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919509 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919509/0 /scratch/stefan/7775247/working/building/REAL300004919509 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/512 `/scratch/stefan/7775247/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=CC(C)=CC(Br)=C2O1)C(=O)[O-]) `REAL300004919509.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919509 none CC#CCC(NC(=O)C1=CC2=CC(C)=CC(Br)=C2O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 5, 1, 1, 17, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 37, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 50, 50, 66, 66, 66, 66, 66, 37, 13, 1, 1, 2, 2, 2, 1] 66 rigid atoms, others: [34, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 32, 33, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 328 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919509 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919509 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919509/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919509 Building REAL300004919510 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919510' /scratch/stefan/7775247/working/building/REAL300004919510 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919510 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919510/0 /scratch/stefan/7775247/working/building/REAL300004919510 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 513) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/513 `/scratch/stefan/7775247/working/3D/513' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=C([N+](=O)[O-])C=C1Br)C(=O)[O-]) `REAL300004919510.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919510 none CC#CCC(NC(=O)CC1=CC=C([N+](=O)[O-])C=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 94, 39, 39, 6, 39, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 94, 139, 139, 201, 201, 201, 201, 201, 94, 39, 6, 6, 1, 1, 1] 201 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 1008 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919510 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919510 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919510/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919510 Building REAL300004919511 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919511' /scratch/stefan/7775247/working/building/REAL300004919511 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919511 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919511/0 /scratch/stefan/7775247/working/building/REAL300004919511 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/514 `/scratch/stefan/7775247/working/3D/514' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC([N+](=O)[O-])=C1N1CCOCC1)C(=O)[O-]) `REAL300004919511.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919511 none CC#CCC(NC(=O)C1=CC=CC([N+](=O)[O-])=C1N1CCOCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 5, 5, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 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, 10, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 2, 2, 10, 12, 12, 18, 18, 18, 18, 18, 10, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2] 18 rigid atoms, others: [33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 16, 17] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919511 none CC#CCC(NC(=O)C1=CC=CC([N+](=O)[O-])=C1N1CCOCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 11, 1, 8, 5, 5, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 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, 10, 3, 3, 2, 3, 2, 2, 1, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 10, 12, 12, 18, 18, 18, 18, 18, 10, 3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1] 18 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919511 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919511 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919511/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919511 Building REAL300004919512 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919512' /scratch/stefan/7775247/working/building/REAL300004919512 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919512 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919512/0 /scratch/stefan/7775247/working/building/REAL300004919512 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 515) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/515 `/scratch/stefan/7775247/working/3D/515' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CC=C(C)O2)S1)C(=O)[O-]) `REAL300004919512.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919512 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(C)O2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 111, 41, 13, 12, 1, 12, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 41, 61, 61, 111, 111, 111, 111, 111, 41, 13, 1, 1, 13, 13, 13, 13, 13] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 515 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919512 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(C)O2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 128, 70, 70, 13, 70, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 128, 159, 159, 201, 201, 201, 201, 201, 128, 70, 13, 13, 1, 1, 2, 2, 2] 201 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 934 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919512 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919512 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919512/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919512 Building REAL300004919513 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919513' /scratch/stefan/7775247/working/building/REAL300004919513 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919513 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919513/0 /scratch/stefan/7775247/working/building/REAL300004919513 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/516 `/scratch/stefan/7775247/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CC(=O)N(C)C1C1=CC=C(F)C=C1)C(=O)[O-]) `REAL300004919513.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919513 none CC#CCC(NC(=O)C1CC(=O)N(C)C1C1=CC=C(F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2, 12, 17, 17, 24, 24, 24, 24, 24, 12, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2] 24 rigid atoms, others: [32, 33, 34, 38, 6, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 39, 40, 41, 42]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919513 none CC#CCC(NC(=O)C1CC(=O)N(C)C1C1=CC=C(F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 12, 4, 4, 2, 4, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 12, 17, 17, 24, 24, 24, 24, 24, 12, 4, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1] 24 rigid atoms, others: [39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 124 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919513 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919513 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919513/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919513 Building REAL300004919514 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919514' /scratch/stefan/7775247/working/building/REAL300004919514 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919514 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919514/0 /scratch/stefan/7775247/working/building/REAL300004919514 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 517) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/517 `/scratch/stefan/7775247/working/3D/517' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NOC(COC2=C(Cl)C=CC=C2Cl)=C1)C(=O)[O-]) `REAL300004919514.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919514 none CC#CCC(NC(=O)C1=NOC(COC2=C(Cl)C=CC=C2Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 12, 1, 5, 12, 1, 1, 16, 1, 1, 1, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 1, 5, 1, 1, 1, 1, 1, 8, 30, 30, 31, 30, 30, 31, 30, 31, 1, 12, 19, 19, 23, 23, 23, 23, 23, 12, 5, 8, 8, 31, 30, 31, 1] 201 rigid atoms, others: [38, 6, 8, 9, 10, 11, 12, 22] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919514 none CC#CCC(NC(=O)C1=NOC(COC2=C(Cl)C=CC=C2Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 12, 1, 5, 12, 1, 1, 16, 1, 1, 1, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 135, 73, 73, 30, 73, 30, 30, 30, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 135, 163, 163, 201, 201, 201, 201, 201, 135, 73, 5, 5, 1, 1, 1, 31] 201 rigid atoms, others: [35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38]) total number of confs: 904 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919514 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919514 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919514/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919514 Building REAL300004919515 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919515' /scratch/stefan/7775247/working/building/REAL300004919515 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919515 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919515/0 /scratch/stefan/7775247/working/building/REAL300004919515 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/518 `/scratch/stefan/7775247/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=CC(OCC2=CC=CN=C2)=C1)C(=O)[O-]) `REAL300004919515.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919515 none CC#CCC(NC(=O)CC1=CC=CC(OCC2=CC=CN=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 4, 13, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 11, 11, 11, 11, 1, 25, 43, 43, 50, 50, 50, 50, 50, 25, 13, 4, 4, 1, 1, 1, 3, 3, 11, 11, 11, 11, 1] 201 rigid atoms, others: [35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 44, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919515 none CC#CCC(NC(=O)CC1=CC=CC(OCC2=CC=CN=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 127, 73, 73, 33, 73, 11, 11, 8, 11, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 127, 158, 158, 201, 201, 201, 201, 201, 127, 73, 33, 33, 8, 11, 11, 8, 8, 1, 1, 1, 1, 11] 201 rigid atoms, others: [40, 41, 42, 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, 44]) total number of confs: 1025 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919515 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919515 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919515/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919515 Building REAL300004919516 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919516' /scratch/stefan/7775247/working/building/REAL300004919516 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919516 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919516/0 /scratch/stefan/7775247/working/building/REAL300004919516 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 519) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/519 `/scratch/stefan/7775247/working/3D/519' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CSC(CC2=CC=C(C)C=C2)=N1)C(=O)[O-]) `REAL300004919516.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919516 none CC#CCC(NC(=O)C1=CSC(CC2=CC=C(C)C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 14, 1, 5, 1, 1, 1, 1, 5, 1, 1, 8, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 19, 8, 8, 1, 8, 1, 1, 1, 1, 1, 8, 18, 18, 18, 18, 18, 18, 1, 19, 31, 31, 59, 59, 59, 59, 59, 19, 8, 1, 8, 8, 18, 18, 18, 18, 18, 18, 18] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 309 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919516 none CC#CCC(NC(=O)C1=CSC(CC2=CC=C(C)C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 14, 1, 5, 1, 1, 1, 1, 5, 1, 1, 8, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 102, 47, 47, 18, 47, 18, 18, 18, 5, 1, 1, 1, 1, 1, 1, 1, 1, 18, 102, 143, 143, 201, 201, 201, 201, 201, 102, 47, 18, 5, 5, 1, 1, 2, 2, 2, 1, 1] 201 rigid atoms, others: [34, 35, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 994 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919516 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919516 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919516/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919516 Building REAL300004919517 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919517' /scratch/stefan/7775247/working/building/REAL300004919517 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919517 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919517/0 /scratch/stefan/7775247/working/building/REAL300004919517 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/520 `/scratch/stefan/7775247/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=NC(OC(C)CC)=C1)C(=O)[O-]) `REAL300004919517.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919517 none CC#CCC(NC(=O)C1=CC=NC(OC(C)CC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 8, 1, 12, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 10, 19, 19, 26, 1, 17, 26, 26, 53, 53, 53, 53, 53, 17, 5, 1, 1, 19, 19, 19, 19, 27, 27, 27, 27, 27, 1] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 40, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 335 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919517 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919517 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919517/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919517 Building REAL300004919518 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919518' /scratch/stefan/7775247/working/building/REAL300004919518 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919518 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919518/0 /scratch/stefan/7775247/working/building/REAL300004919518 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 521) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/521 `/scratch/stefan/7775247/working/3D/521' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CSC(CC2=CC=CC(F)=C2)=N1)C(=O)[O-]) `REAL300004919518.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919518 none CC#CCC(NC(=O)C1=CSC(CC2=CC=CC(F)=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 5, 1, 1, 1, 1, 1, 15, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 3, 3, 1, 3, 1, 1, 1, 1, 1, 9, 28, 28, 28, 28, 28, 28, 1, 10, 15, 15, 26, 26, 26, 26, 26, 10, 4, 1, 9, 9, 28, 28, 28, 28] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919518 none CC#CCC(NC(=O)C1=CSC(CC2=CC=CC(F)=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 5, 1, 1, 1, 1, 1, 15, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 97, 48, 48, 28, 48, 28, 28, 28, 6, 1, 1, 1, 1, 1, 1, 1, 1, 28, 97, 144, 144, 201, 201, 201, 201, 201, 97, 48, 28, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 1043 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919518 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919518 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919518/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919518 Building REAL300004919519 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919519' /scratch/stefan/7775247/working/building/REAL300004919519 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919519 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919519/0 /scratch/stefan/7775247/working/building/REAL300004919519 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/522 `/scratch/stefan/7775247/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2CCCC2)N=C1)C(=O)[O-]) `REAL300004919519.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919519 none CC#CCC(NC(=O)C1=C(C)N(C2CCCC2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 8, 5, 5, 5, 5, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 119, 48, 13, 13, 1, 13, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 48, 79, 79, 119, 119, 119, 119, 119, 48, 13, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 17, 18, 41] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 610 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: REAL300004919519 none CC#CCC(NC(=O)C1=C(C)N(C2CCCC2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 8, 5, 5, 5, 5, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 123, 54, 54, 6, 54, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 123, 154, 154, 201, 201, 201, 201, 201, 123, 54, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41]) total number of confs: 927 number of broken/clashed sets: 43 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919519 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919519 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919519/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919519 Building REAL300004919520 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919520' /scratch/stefan/7775247/working/building/REAL300004919520 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919520 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919520/0 /scratch/stefan/7775247/working/building/REAL300004919520 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 523) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/523 `/scratch/stefan/7775247/working/3D/523' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C2CC2)N(C(C)CC)N=C1)C(=O)[O-]) `REAL300004919520.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919520 none CC#CCC(NC(=O)C1=C(C2CC2)N(C(C)CC)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 5, 5, 8, 5, 5, 5, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 116, 44, 13, 13, 1, 13, 1, 1, 1, 4, 4, 1, 1, 5, 5, 8, 1, 1, 44, 71, 71, 116, 116, 116, 116, 116, 44, 13, 4, 4, 4, 4, 4, 5, 5, 5, 5, 10, 10, 10, 10, 10, 1] 201 rigid atoms, others: [6, 8, 9, 10, 44, 13, 14, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 621 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: REAL300004919520 none CC#CCC(NC(=O)C1=C(C2CC2)N(C(C)CC)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 5, 5, 8, 5, 5, 5, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [136, 136, 136, 59, 20, 20, 4, 20, 4, 1, 1, 1, 1, 4, 4, 9, 9, 13, 4, 4, 59, 93, 93, 136, 136, 136, 136, 136, 59, 20, 1, 1, 1, 1, 1, 9, 9, 9, 9, 14, 14, 14, 14, 14, 4] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 30, 31] 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 737 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919520 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919520 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919520/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919520 Building REAL300004919521 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919521' /scratch/stefan/7775247/working/building/REAL300004919521 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919521 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919521/0 /scratch/stefan/7775247/working/building/REAL300004919521 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/524 `/scratch/stefan/7775247/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(Cl)C=C1OCC)C(=O)[O-]) `REAL300004919521.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919521 none CC#CCC(NC(=O)C1=CC=C(Cl)C=C1OCC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 110, 37, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 9, 30, 37, 60, 60, 110, 110, 110, 110, 110, 37, 12, 1, 1, 1, 30, 30, 30, 30, 30] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 600 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919521 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919521 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919521/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919521 Building REAL300004919522 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919522' /scratch/stefan/7775247/working/building/REAL300004919522 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919522 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919522/0 /scratch/stefan/7775247/working/building/REAL300004919522 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 525) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/525 `/scratch/stefan/7775247/working/3D/525' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOC1=CC(OC)=CC=C1C(=O)NC(CC#CC)C(=O)[O-]) `REAL300004919522.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919522 none C=CCOC1=CC(OC)=CC=C1C(=O)NC(CC#CC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.1', 'C.1', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 5, 1, 11, 11, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [74, 31, 7, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 10, 10, 10, 16, 43, 43, 43, 16, 18, 18, 74, 74, 74, 31, 31, 1, 3, 3, 3, 1, 1, 10, 16, 43, 43, 43, 43, 43] 162 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 9, 10, 11, 12, 28] set([0, 1, 2, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 408 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919522 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919522 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919522/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919522 Building REAL300004919523 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919523' /scratch/stefan/7775247/working/building/REAL300004919523 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919523 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919523/0 /scratch/stefan/7775247/working/building/REAL300004919523 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/526 `/scratch/stefan/7775247/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NC=CC=C1OCC(F)(F)F)C(=O)[O-]) `REAL300004919523.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919523 none CC#CCC(NC(=O)C1=NC=CC=C1OCC(F)(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.3', 'F', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 31, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 9, 26, 26, 26, 26, 31, 52, 52, 88, 88, 88, 88, 88, 31, 11, 1, 1, 1, 26, 26] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 512 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919523 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919523 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919523/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919523 Building REAL300004919524 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919524' /scratch/stefan/7775247/working/building/REAL300004919524 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919524 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919524/0 /scratch/stefan/7775247/working/building/REAL300004919524 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 527) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/527 `/scratch/stefan/7775247/working/3D/527' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=C(C)C=C2)C(C)=C1)C(=O)[O-]) `REAL300004919524.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919524 none CC#CCC(NC(=O)C1=NN(C2=CC=C(C)C=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 33, 11, 11, 1, 11, 1, 1, 1, 1, 5, 5, 1, 1, 5, 5, 1, 1, 1, 33, 52, 52, 93, 93, 93, 93, 93, 33, 11, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 1] 123 rigid atoms, others: [6, 8, 9, 10, 11, 18, 19, 20, 41] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 461 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: REAL300004919524 none CC#CCC(NC(=O)C1=NN(C2=CC=C(C)C=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [123, 123, 123, 57, 25, 25, 5, 25, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 57, 79, 79, 123, 123, 123, 123, 123, 57, 25, 1, 1, 2, 2, 2, 1, 1, 5, 5, 5, 5] 123 rigid atoms, others: [32, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 567 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919524 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919524 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919524/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919524 Building REAL300004919525 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919525' /scratch/stefan/7775247/working/building/REAL300004919525 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919525 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919525/0 /scratch/stefan/7775247/working/building/REAL300004919525 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/528 `/scratch/stefan/7775247/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=C(Cl)C=C2Cl)C(C)=C1)C(=O)[O-]) `REAL300004919525.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919525 none CC#CCC(NC(=O)C1=NN(C2=CC=C(Cl)C=C2Cl)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 16, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [109, 109, 109, 40, 11, 11, 1, 11, 1, 1, 1, 1, 7, 7, 1, 4, 7, 7, 7, 1, 1, 1, 40, 66, 66, 109, 109, 109, 109, 109, 40, 11, 7, 7, 7, 2, 2, 2, 1] 184 rigid atoms, others: [38, 6, 8, 9, 10, 11, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 551 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919525 none CC#CCC(NC(=O)C1=NN(C2=CC=C(Cl)C=C2Cl)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 16, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [184, 184, 184, 108, 45, 45, 7, 45, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 108, 137, 137, 184, 184, 184, 184, 184, 108, 45, 1, 1, 1, 7, 7, 7, 7] 184 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 836 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919525 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919525 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919525/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919525 Building REAL300004919526 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919526' /scratch/stefan/7775247/working/building/REAL300004919526 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919526 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919526/0 /scratch/stefan/7775247/working/building/REAL300004919526 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 529) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/529 `/scratch/stefan/7775247/working/3D/529' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=C(Cl)C(Cl)=C2)C(C)=C1)C(=O)[O-]) `REAL300004919526.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919526 none CC#CCC(NC(=O)C1=NN(C2=CC=C(Cl)C(Cl)=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 26, 9, 9, 1, 9, 1, 1, 1, 1, 7, 7, 4, 7, 7, 7, 7, 1, 1, 1, 26, 40, 40, 61, 61, 61, 61, 61, 26, 9, 7, 7, 7, 2, 2, 2, 1] 201 rigid atoms, others: [38, 6, 8, 9, 10, 11, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 331 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: REAL300004919526 none CC#CCC(NC(=O)C1=NN(C2=CC=C(Cl)C(Cl)=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 16, 1, 16, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 91, 37, 37, 7, 37, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 91, 127, 127, 201, 201, 201, 201, 201, 91, 37, 1, 1, 1, 7, 7, 7, 7] 201 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 955 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919526 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919526 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919526/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919526 Building REAL300004919527 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919527' /scratch/stefan/7775247/working/building/REAL300004919527 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919527 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919527/0 /scratch/stefan/7775247/working/building/REAL300004919527 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/530 `/scratch/stefan/7775247/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=C(OC)C=C2)C(C)=C1)C(=O)[O-]) `REAL300004919527.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919527 none CC#CCC(NC(=O)C1=NN(C2=CC=C(OC)C=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 28, 10, 10, 1, 10, 1, 1, 1, 1, 5, 5, 1, 1, 8, 5, 5, 1, 1, 1, 28, 44, 44, 91, 91, 91, 91, 91, 28, 10, 5, 5, 8, 8, 8, 5, 5, 2, 2, 2, 1] 201 rigid atoms, others: [6, 8, 9, 10, 11, 19, 20, 21, 42] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 443 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: REAL300004919527 none CC#CCC(NC(=O)C1=NN(C2=CC=C(OC)C=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [162, 162, 162, 55, 22, 22, 5, 22, 5, 5, 1, 1, 1, 1, 1, 1, 2, 1, 1, 5, 5, 5, 55, 85, 85, 162, 162, 162, 162, 162, 55, 22, 1, 1, 3, 3, 3, 1, 1, 5, 5, 5, 5] 201 rigid atoms, others: [32, 33, 37, 38, 10, 11, 12, 13, 14, 15, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 772 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919527 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919527 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919527/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919527 Building REAL300004919528 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919528' /scratch/stefan/7775247/working/building/REAL300004919528 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919528 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919528/0 /scratch/stefan/7775247/working/building/REAL300004919528 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 531) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/531 `/scratch/stefan/7775247/working/3D/531' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=NC=C1Br)C(=O)[O-]) `REAL300004919528.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919528 none CC#CCC(NC(=O)C1=CC=NC=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 22, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 22, 36, 36, 60, 60, 60, 60, 60, 22, 7, 1, 1, 1] 60 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 287 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919528 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919528 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919528/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919528 Building REAL300004919529 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919529' /scratch/stefan/7775247/working/building/REAL300004919529 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919529 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919529/0 /scratch/stefan/7775247/working/building/REAL300004919529 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/532 `/scratch/stefan/7775247/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C2=CC=CC=C2)=NC2=CC=CC=C21)C(=O)[O-]) `REAL300004919529.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919529 none CC#CCC(NC(=O)C1=CC(C2=CC=CC=C2)=NC2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 116, 38, 9, 9, 1, 9, 1, 1, 1, 1, 7, 7, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 38, 62, 62, 116, 116, 116, 116, 116, 38, 9, 1, 7, 7, 3, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [41, 34, 43, 40, 6, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39]) total number of confs: 551 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919529 none CC#CCC(NC(=O)C1=CC(C2=CC=CC=C2)=NC2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 122, 46, 46, 7, 46, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 122, 151, 151, 201, 201, 201, 201, 201, 122, 46, 7, 1, 1, 1, 1, 1, 7, 7, 7, 7] 201 rigid atoms, others: [35, 36, 37, 38, 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, 40, 41, 42, 43]) total number of confs: 937 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919529 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919529 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919529/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919529 Building REAL300004919530 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919530' /scratch/stefan/7775247/working/building/REAL300004919530 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919530 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919530/0 /scratch/stefan/7775247/working/building/REAL300004919530 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 533) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/533 `/scratch/stefan/7775247/working/3D/533' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C2=CC=C(Cl)C=C2)=NC2=CC=CC=C21)C(=O)[O-]) `REAL300004919530.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919530 none CC#CCC(NC(=O)C1=CC(C2=CC=C(Cl)C=C2)=NC2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 120, 120, 39, 9, 9, 1, 9, 1, 1, 1, 1, 7, 7, 3, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 39, 60, 60, 120, 120, 120, 120, 120, 39, 9, 1, 7, 7, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [35, 6, 8, 9, 10, 11, 43, 40, 18, 19, 20, 21, 22, 41, 24, 23, 42] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39]) total number of confs: 553 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919530 none CC#CCC(NC(=O)C1=CC(C2=CC=C(Cl)C=C2)=NC2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 123, 45, 45, 7, 45, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 123, 154, 154, 201, 201, 201, 201, 201, 123, 45, 7, 1, 1, 1, 1, 7, 7, 7, 7] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43]) total number of confs: 952 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919530 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919530 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919530/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919530 Building REAL300004919531 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919531' /scratch/stefan/7775247/working/building/REAL300004919531 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919531 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919531/0 /scratch/stefan/7775247/working/building/REAL300004919531 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/534 `/scratch/stefan/7775247/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1C2=CC=CC=C2OC2=CC=CC=C21)C(=O)[O-]) `REAL300004919531.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919531 none CC#CCC(NC(=O)C1C2=CC=CC=C2OC2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [83, 83, 83, 41, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 54, 54, 83, 83, 83, 83, 83, 41, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1] 83 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 7, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 383 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919531 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919531 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919531/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919531 Building REAL300004919532 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919532' /scratch/stefan/7775247/working/building/REAL300004919532 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919532 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919532/0 /scratch/stefan/7775247/working/building/REAL300004919532 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 535) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/535 `/scratch/stefan/7775247/working/3D/535' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C2=CC=CS2)=NC2=CC=CC=C21)C(=O)[O-]) `REAL300004919532.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919532 none CC#CCC(NC(=O)C1=CC(C2=CC=CS2)=NC2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 14, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 28, 9, 9, 1, 9, 1, 1, 1, 1, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 28, 47, 47, 76, 76, 76, 76, 76, 28, 9, 1, 11, 11, 11, 1, 1, 1, 1] 201 rigid atoms, others: [33, 37, 6, 39, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36]) total number of confs: 391 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919532 none CC#CCC(NC(=O)C1=CC(C2=CC=CS2)=NC2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 14, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 68, 68, 11, 68, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 131, 153, 153, 201, 201, 201, 201, 201, 131, 68, 11, 1, 1, 1, 12, 12, 11, 11] 201 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 888 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919532 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919532 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919532/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919532 Building REAL300004919533 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919533' /scratch/stefan/7775247/working/building/REAL300004919533 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919533 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919533/0 /scratch/stefan/7775247/working/building/REAL300004919533 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/536 `/scratch/stefan/7775247/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CC=C(Cl)C(Cl)=C2)S1)C(=O)[O-]) `REAL300004919533.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919533 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(Cl)C(Cl)=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 16, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 28, 9, 9, 1, 9, 1, 1, 1, 1, 1, 13, 13, 1, 12, 13, 13, 13, 1, 28, 44, 44, 71, 71, 71, 71, 71, 28, 10, 1, 1, 13, 13, 13] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 379 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919533 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(Cl)C(Cl)=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 16, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 125, 69, 69, 13, 68, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 125, 147, 147, 201, 201, 201, 201, 201, 125, 69, 13, 13, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 877 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919533 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919533 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919533/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919533 Building REAL300004919534 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919534' /scratch/stefan/7775247/working/building/REAL300004919534 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919534 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919534/0 /scratch/stefan/7775247/working/building/REAL300004919534 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 537) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/537 `/scratch/stefan/7775247/working/3D/537' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=NC(OCC2=CC=CC=C2)=C1)C(=O)[O-]) `REAL300004919534.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919534 none CC#CCC(NC(=O)C1=CC=NC(OCC2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 8, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 20, 35, 35, 23, 35, 35, 1, 14, 22, 22, 45, 45, 45, 45, 45, 14, 5, 1, 1, 20, 20, 35, 35, 35, 35, 35, 1] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 21, 41] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 340 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919534 none CC#CCC(NC(=O)C1=CC=NC(OCC2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 8, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 87, 87, 35, 87, 35, 34, 35, 35, 17, 3, 1, 1, 1, 1, 1, 1, 1, 35, 137, 161, 161, 201, 201, 201, 201, 201, 137, 87, 34, 35, 3, 3, 1, 1, 1, 1, 1, 35] 201 rigid atoms, others: [36, 37, 38, 39, 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, 41]) total number of confs: 887 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919534 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919534 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919534/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919534 Building REAL300004919535 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919535' /scratch/stefan/7775247/working/building/REAL300004919535 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919535 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919535/0 /scratch/stefan/7775247/working/building/REAL300004919535 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/538 `/scratch/stefan/7775247/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C2=CC=C(C)C=C2)=NC2=CC=CC=C21)C(=O)[O-]) `REAL300004919535.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919535 none CC#CCC(NC(=O)C1=CC(C2=CC=C(C)C=C2)=NC2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 39, 9, 9, 1, 9, 1, 1, 1, 1, 7, 7, 1, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 39, 60, 60, 118, 118, 118, 118, 118, 39, 9, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [35, 6, 8, 9, 10, 11, 44, 45, 43, 18, 19, 20, 21, 22, 23, 24, 46] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 562 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: REAL300004919535 none CC#CCC(NC(=O)C1=CC(C2=CC=C(C)C=C2)=NC2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 122, 45, 45, 7, 45, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 122, 152, 152, 201, 201, 201, 201, 201, 122, 45, 7, 1, 1, 2, 2, 2, 1, 1, 7, 7, 7, 7] 201 rigid atoms, others: [36, 37, 41, 10, 11, 12, 13, 14, 15, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 43, 44, 45, 46]) total number of confs: 957 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919535 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919535 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919535/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919535 Building REAL300004919536 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919536' /scratch/stefan/7775247/working/building/REAL300004919536 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919536 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919536/0 /scratch/stefan/7775247/working/building/REAL300004919536 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 539) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/539 `/scratch/stefan/7775247/working/3D/539' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CNC(=O)C1=CC=C(OC)C=C1)C(=O)[O-]) `REAL300004919536.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919536 none CC#CCC(NC(=O)CNC(=O)C1=CC=C(OC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [162, 162, 162, 105, 62, 62, 15, 62, 3, 3, 1, 3, 1, 1, 1, 1, 1, 2, 1, 1, 105, 151, 151, 162, 162, 162, 162, 162, 105, 62, 15, 15, 3, 1, 1, 3, 3, 3, 1, 1] 201 rigid atoms, others: [33, 34, 38, 39, 10, 12, 13, 14, 15, 16, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 894 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919536 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919536 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919536/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919536 Building REAL300004919537 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919537' /scratch/stefan/7775247/working/building/REAL300004919537 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919537 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919537/0 /scratch/stefan/7775247/working/building/REAL300004919537 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/540 `/scratch/stefan/7775247/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1NC1=CC=CC(C(F)(F)F)=C1)C(=O)[O-]) `REAL300004919537.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919537 none CC#CCC(NC(=O)C1=CC=CC=C1NC1=CC=CC(C(F)(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 25, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 6, 24, 24, 6, 24, 24, 24, 24, 24, 24, 25, 38, 38, 57, 57, 57, 57, 57, 25, 10, 1, 1, 1, 1, 6, 24, 24, 6, 24] 201 rigid atoms, others: [35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 38] set([0, 1, 2, 3, 4, 5, 7, 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: 349 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919537 none CC#CCC(NC(=O)C1=CC=CC=C1NC1=CC=CC(C(F)(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 71, 71, 24, 71, 24, 24, 24, 24, 24, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 131, 164, 164, 201, 201, 201, 201, 201, 131, 71, 24, 24, 24, 24, 12, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 14, 15, 16, 17, 18, 19, 20, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 964 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919537 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919537 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919537/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919537 Building REAL300004919538 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919538' /scratch/stefan/7775247/working/building/REAL300004919538 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919538 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919538/0 /scratch/stefan/7775247/working/building/REAL300004919538 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 541) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/541 `/scratch/stefan/7775247/working/3D/541' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CNC(=O)C1=CC=C(OC)C(OC)=C1)C(=O)[O-]) `REAL300004919538.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919538 none CC#CCC(NC(=O)CNC(=O)C1=CC=C(OC)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 125, 103, 60, 60, 20, 64, 5, 5, 1, 5, 1, 1, 1, 1, 1, 3, 1, 1, 3, 1, 103, 104, 104, 125, 125, 125, 125, 125, 103, 64, 20, 20, 5, 1, 1, 4, 4, 4, 4, 4, 4, 1] 201 rigid atoms, others: [35, 36, 10, 43, 12, 13, 14, 15, 16, 18, 19, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42]) total number of confs: 539 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919538 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919538 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919538/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919538 Building REAL300004919539 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919539' /scratch/stefan/7775247/working/building/REAL300004919539 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919539 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919539/0 /scratch/stefan/7775247/working/building/REAL300004919539 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/542 `/scratch/stefan/7775247/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CNC(=O)C1=CC=C(C(C)(C)C)C=C1)C(=O)[O-]) `REAL300004919539.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919539 none CC#CCC(NC(=O)CNC(=O)C1=CC=C(C(C)(C)C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [160, 160, 160, 102, 63, 63, 15, 63, 3, 3, 1, 3, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 102, 155, 155, 160, 160, 160, 160, 160, 102, 63, 15, 15, 3, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1] 201 rigid atoms, others: [35, 36, 10, 46, 12, 13, 14, 15, 16, 20, 21, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 937 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919539 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919539 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919539/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919539 Building REAL300004919540 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919540' /scratch/stefan/7775247/working/building/REAL300004919540 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919540 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919540/0 /scratch/stefan/7775247/working/building/REAL300004919540 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 543) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/543 `/scratch/stefan/7775247/working/3D/543' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C2CCCC2=NC2=CC=CC=C21)C(=O)[O-]) `REAL300004919540.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919540 none CC#CCC(NC(=O)C1=C2CCCC2=NC2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 30, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 45, 45, 73, 73, 73, 73, 73, 30, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 73 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 7, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919540 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919540 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919540/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919540 Building REAL300004919541 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919541' /scratch/stefan/7775247/working/building/REAL300004919541 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919541 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919541/0 /scratch/stefan/7775247/working/building/REAL300004919541 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/544 `/scratch/stefan/7775247/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C2=CC=C(Cl)S2)=NC2=CC=CC=C21)C(=O)[O-]) `REAL300004919541.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919541 none CC#CCC(NC(=O)C1=CC(C2=CC=C(Cl)S2)=NC2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 16, 14, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 26, 9, 9, 1, 9, 1, 1, 1, 1, 12, 12, 11, 12, 12, 1, 1, 1, 1, 1, 1, 1, 26, 44, 44, 80, 80, 80, 80, 80, 26, 9, 1, 12, 12, 1, 1, 1, 1] 201 rigid atoms, others: [34, 37, 6, 39, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36]) total number of confs: 411 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919541 none CC#CCC(NC(=O)C1=CC(C2=CC=C(Cl)S2)=NC2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 16, 14, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 143, 74, 74, 12, 74, 12, 12, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 11, 11, 143, 167, 167, 201, 201, 201, 201, 201, 143, 74, 12, 1, 1, 12, 12, 12, 12] 201 rigid atoms, others: [35, 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, 37, 38, 39, 40]) total number of confs: 911 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919541 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919541 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919541/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919541 Building REAL300004919542 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919542' /scratch/stefan/7775247/working/building/REAL300004919542 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919542 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919542/0 /scratch/stefan/7775247/working/building/REAL300004919542 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 545) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/545 `/scratch/stefan/7775247/working/3D/545' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CNC(=O)C1=CC=CC=C1OCC)C(=O)[O-]) `REAL300004919542.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919542 none CC#CCC(NC(=O)CNC(=O)C1=CC=CC=C1OCC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 158, 90, 53, 53, 15, 54, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 5, 15, 90, 128, 128, 158, 158, 158, 158, 158, 90, 54, 15, 15, 6, 1, 1, 1, 1, 15, 15, 15, 15, 15] 201 rigid atoms, others: [34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 879 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919542 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919542 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919542/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919542 Building REAL300004919543 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919543' /scratch/stefan/7775247/working/building/REAL300004919543 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919543 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919543/0 /scratch/stefan/7775247/working/building/REAL300004919543 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/546 `/scratch/stefan/7775247/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CNC(=O)C1=CC=CC(F)=C1)C(=O)[O-]) `REAL300004919543.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919543 none CC#CCC(NC(=O)CNC(=O)C1=CC=CC(F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 82, 82, 20, 82, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 131, 169, 169, 201, 201, 201, 201, 201, 131, 82, 20, 20, 5, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 994 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919543 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919543 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919543/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919543 Building REAL300004919544 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919544' /scratch/stefan/7775247/working/building/REAL300004919544 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919544 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919544/0 /scratch/stefan/7775247/working/building/REAL300004919544 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 547) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/547 `/scratch/stefan/7775247/working/3D/547' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CNC(=O)C1=CC=CC(Br)=C1)C(=O)[O-]) `REAL300004919544.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919544 none CC#CCC(NC(=O)CNC(=O)C1=CC=CC(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 129, 81, 81, 20, 81, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 129, 168, 168, 201, 201, 201, 201, 201, 129, 81, 20, 20, 5, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 1008 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919544 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919544 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919544/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919544 Building REAL300004919545 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919545' /scratch/stefan/7775247/working/building/REAL300004919545 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919545 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919545/0 /scratch/stefan/7775247/working/building/REAL300004919545 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/548 `/scratch/stefan/7775247/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CNC(=O)C1=CC=CC(OC)=C1)C(=O)[O-]) `REAL300004919545.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919545 none CC#CCC(NC(=O)CNC(=O)C1=CC=CC(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [182, 182, 182, 106, 64, 64, 19, 64, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 3, 1, 106, 147, 147, 182, 182, 182, 182, 182, 106, 64, 19, 19, 5, 1, 1, 1, 3, 3, 3, 1] 201 rigid atoms, others: [33, 34, 35, 39, 10, 12, 13, 14, 15, 16, 17, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 938 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919545 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919545 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919545/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919545 Building REAL300004919546 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919546' /scratch/stefan/7775247/working/building/REAL300004919546 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919546 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919546/0 /scratch/stefan/7775247/working/building/REAL300004919546 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 549) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/549 `/scratch/stefan/7775247/working/3D/549' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CNC(=O)C1=CC=C2OCOC2=C1)C(=O)[O-]) `REAL300004919546.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919546 none CC#CCC(NC(=O)CNC(=O)C1=CC=C2OCOC2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 126, 77, 77, 18, 77, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 126, 169, 169, 201, 201, 201, 201, 201, 126, 77, 18, 18, 5, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 1034 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919546 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919546 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919546/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919546 Building REAL300004919547 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919547' /scratch/stefan/7775247/working/building/REAL300004919547 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919547 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919547/0 /scratch/stefan/7775247/working/building/REAL300004919547 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/550 `/scratch/stefan/7775247/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CNC(=O)C1=CC=C(OCC)C=C1)C(=O)[O-]) `REAL300004919547.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919547 none CC#CCC(NC(=O)CNC(=O)C1=CC=C(OCC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 111, 74, 48, 48, 15, 48, 3, 3, 1, 3, 1, 1, 1, 1, 1, 6, 9, 1, 1, 74, 107, 107, 111, 111, 111, 111, 111, 74, 48, 15, 15, 3, 1, 1, 9, 9, 9, 9, 9, 1, 1] 201 rigid atoms, others: [34, 35, 41, 10, 12, 13, 14, 15, 16, 19, 20, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40]) total number of confs: 640 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919547 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919547 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919547/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919547 Building REAL300004919548 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919548' /scratch/stefan/7775247/working/building/REAL300004919548 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919548 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919548/0 /scratch/stefan/7775247/working/building/REAL300004919548 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 551) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/551 `/scratch/stefan/7775247/working/3D/551' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CNC(=O)C1=CC=C([N+](=O)[O-])C(C)=C1)C(=O)[O-]) `REAL300004919548.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919548 none CC#CCC(NC(=O)CNC(=O)C1=CC=C([N+](=O)[O-])C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 128, 81, 81, 21, 81, 5, 5, 1, 5, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 128, 174, 174, 201, 201, 201, 201, 201, 128, 81, 21, 21, 5, 1, 1, 2, 2, 2, 1] 201 rigid atoms, others: [35, 36, 40, 10, 12, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39]) total number of confs: 1059 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919548 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919548 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919548/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919548 Building REAL300004919549 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919549' /scratch/stefan/7775247/working/building/REAL300004919549 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919549 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919549/0 /scratch/stefan/7775247/working/building/REAL300004919549 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/552 `/scratch/stefan/7775247/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=C(Br)C=C1C)C(=O)[O-]) `REAL300004919549.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919549 none CC#CCC(NC(=O)CC1=CC=C(Br)C=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 17, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 91, 39, 39, 6, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 91, 133, 133, 201, 201, 201, 201, 201, 91, 39, 6, 6, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 980 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919549 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919549 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919549/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919549 Building REAL300004919550 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919550' /scratch/stefan/7775247/working/building/REAL300004919550 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919550 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919550/0 /scratch/stefan/7775247/working/building/REAL300004919550 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 553) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/553 `/scratch/stefan/7775247/working/3D/553' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC)C(C2=CC=CC=N2)=C1)C(=O)[O-]) `REAL300004919550.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919550 none CC#CCC(NC(=O)C1=CC=C(OC)C(C2=CC=CC=N2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 3, 1, 1, 7, 7, 7, 7, 7, 1, 17, 29, 29, 58, 58, 58, 58, 58, 17, 5, 1, 1, 3, 3, 3, 7, 7, 7, 7, 1] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 14, 15, 21, 41] set([0, 1, 2, 3, 4, 5, 7, 13, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40]) 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: REAL300004919550 none CC#CCC(NC(=O)C1=CC=C(OC)C(C2=CC=CC=N2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [166, 166, 166, 65, 23, 23, 7, 23, 7, 7, 7, 7, 7, 13, 1, 1, 1, 1, 1, 1, 1, 7, 65, 100, 100, 166, 166, 166, 166, 166, 65, 23, 7, 7, 13, 13, 13, 1, 1, 1, 1, 7] 201 rigid atoms, others: [37, 38, 39, 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, 41]) total number of confs: 790 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919550 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919550 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919550/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919550 Building REAL300004919551 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919551' /scratch/stefan/7775247/working/building/REAL300004919551 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919551 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919551/0 /scratch/stefan/7775247/working/building/REAL300004919551 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/554 `/scratch/stefan/7775247/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NOC(CN2C=C(C)C=N2)=C1)C(=O)[O-]) `REAL300004919551.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919551 none CC#CCC(NC(=O)C1=NOC(CN2C=C(C)C=N2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 12, 1, 5, 8, 1, 1, 5, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 8, 35, 35, 35, 35, 35, 1, 11, 20, 20, 34, 34, 34, 34, 34, 11, 4, 8, 8, 35, 35, 35, 35, 35, 1] 201 rigid atoms, others: [37, 6, 8, 9, 10, 11, 12, 19] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919551 none CC#CCC(NC(=O)C1=NOC(CN2C=C(C)C=N2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 12, 1, 5, 8, 1, 1, 5, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 70, 70, 35, 70, 35, 35, 35, 8, 1, 1, 1, 1, 1, 1, 1, 35, 131, 165, 165, 201, 201, 201, 201, 201, 131, 70, 8, 8, 1, 2, 2, 2, 1, 35] 201 rigid atoms, others: [32, 36, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 37]) total number of confs: 952 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919551 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919551 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919551/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919551 Building REAL300004919552 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919552' /scratch/stefan/7775247/working/building/REAL300004919552 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919552 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919552/0 /scratch/stefan/7775247/working/building/REAL300004919552 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 555) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/555 `/scratch/stefan/7775247/working/3D/555' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(C2(C)NC(=O)NC2=O)=C1)C(=O)[O-]) `REAL300004919552.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919552 none CC#CCC(NC(=O)C1=CC=CC(C2(C)NC(=O)NC2=O)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 8, 1, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 1, 17, 29, 29, 50, 50, 50, 50, 50, 17, 5, 1, 1, 1, 13, 13, 13, 13, 13, 1] 201 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 40, 21] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39]) total number of confs: 265 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919552 none CC#CCC(NC(=O)C1=CC=CC(C2(C)NC(=O)NC2=O)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 8, 1, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 100, 42, 42, 13, 42, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 100, 138, 138, 201, 201, 201, 201, 201, 100, 42, 13, 13, 13, 2, 2, 2, 1, 1, 13] 201 rigid atoms, others: [38, 39, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40]) total number of confs: 987 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919552 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919552 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919552/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919552 Building REAL300004919553 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919553' /scratch/stefan/7775247/working/building/REAL300004919553 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919553 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919553/0 /scratch/stefan/7775247/working/building/REAL300004919553 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/556 `/scratch/stefan/7775247/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C2=CC=CC=C2)=NC2=CC(F)=CC=C21)C(=O)[O-]) `REAL300004919553.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919553 none CC#CCC(NC(=O)C1=CC(C2=CC=CC=C2)=NC2=CC(F)=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 39, 9, 9, 1, 9, 1, 1, 1, 1, 7, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 39, 60, 60, 112, 112, 112, 112, 112, 39, 9, 1, 7, 7, 1, 7, 7, 1, 1, 1] 201 rigid atoms, others: [35, 6, 8, 9, 10, 11, 43, 17, 18, 19, 20, 21, 22, 41, 24, 23, 42] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40]) total number of confs: 523 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: REAL300004919553 none CC#CCC(NC(=O)C1=CC(C2=CC=CC=C2)=NC2=CC(F)=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 15, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 44, 44, 7, 44, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 119, 149, 149, 201, 201, 201, 201, 201, 119, 44, 7, 1, 1, 1, 1, 1, 7, 7, 7] 201 rigid atoms, others: [36, 37, 38, 39, 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, 41, 42, 43]) total number of confs: 931 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919553 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919553 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919553/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919553 Building REAL300004919554 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919554' /scratch/stefan/7775247/working/building/REAL300004919554 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919554 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919554/0 /scratch/stefan/7775247/working/building/REAL300004919554 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 557) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/557 `/scratch/stefan/7775247/working/3D/557' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC2=CC=CN=C2)C=C1)C(=O)[O-]) `REAL300004919554.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919554 none CC#CCC(NC(=O)C1=CC=C(OC2=CC=CN=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 9, 27, 27, 27, 27, 27, 1, 1, 7, 11, 11, 19, 19, 19, 19, 19, 7, 3, 1, 1, 27, 27, 27, 27, 1, 1] 201 rigid atoms, others: [32, 37, 6, 8, 9, 10, 11, 12, 19, 20, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919554 none CC#CCC(NC(=O)C1=CC=C(OC2=CC=CN=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 99, 48, 48, 27, 48, 27, 27, 27, 9, 1, 1, 1, 1, 1, 1, 1, 27, 27, 99, 139, 139, 201, 201, 201, 201, 201, 99, 48, 27, 27, 1, 1, 1, 1, 27, 27] 201 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38]) total number of confs: 967 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919554 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919554 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919554/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919554 Building REAL300004919555 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919555' /scratch/stefan/7775247/working/building/REAL300004919555 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919555 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919555/0 /scratch/stefan/7775247/working/building/REAL300004919555 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/558 `/scratch/stefan/7775247/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(NC(C)=O)=CC=C1F)C(=O)[O-]) `REAL300004919555.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919555 none CC#CCC(NC(=O)C1=CC(NC(C)=O)=CC=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 5, 11, 1, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 35, 12, 12, 1, 12, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 35, 55, 55, 95, 95, 95, 95, 95, 35, 12, 1, 4, 4, 4, 4, 1, 1] 201 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 458 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919555 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919555 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919555/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919555 Building REAL300004919556 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919556' /scratch/stefan/7775247/working/building/REAL300004919556 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919556 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919556/0 /scratch/stefan/7775247/working/building/REAL300004919556 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 559) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/559 `/scratch/stefan/7775247/working/3D/559' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(Br)C(C2=CC=CC=C2)=NN1)C(=O)[O-]) `REAL300004919556.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919556 none CC#CCC(NC(=O)C1=C(Br)C(C2=CC=CC=C2)=NN1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 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: [91, 91, 91, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 6, 6, 2, 6, 6, 1, 1, 26, 43, 43, 91, 91, 91, 91, 91, 26, 7, 6, 6, 3, 6, 6, 1] 131 rigid atoms, others: [35, 6, 8, 9, 10, 11, 12, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 429 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919556 none CC#CCC(NC(=O)C1=C(Br)C(C2=CC=CC=C2)=NN1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 17, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [130, 130, 130, 64, 22, 22, 6, 22, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 64, 86, 86, 130, 130, 130, 130, 130, 64, 22, 1, 1, 1, 1, 1, 6] 130 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35]) total number of confs: 602 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919556 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919556 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919556/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919556 Building REAL300004919557 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919557' /scratch/stefan/7775247/working/building/REAL300004919557 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919557 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919557/0 /scratch/stefan/7775247/working/building/REAL300004919557 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/560 `/scratch/stefan/7775247/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CN=C1SC(F)(F)F)C(=O)[O-]) `REAL300004919557.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919557 none CC#CCC(NC(=O)C1=CC=CN=C1SC(F)(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 14, 5, 15, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 4, 4, 4, 6, 6, 6, 6, 6, 4, 4, 1, 1, 1] 6 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 21 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919557 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919557 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919557/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919557 Building REAL300004919558 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919558' /scratch/stefan/7775247/working/building/REAL300004919558 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919558 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919558/0 /scratch/stefan/7775247/working/building/REAL300004919558 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 561) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/561 `/scratch/stefan/7775247/working/3D/561' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC(C)(C)C1=CC=CC=C1)C(=O)[O-]) `REAL300004919558.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919558 none CC#CCC(NC(=O)CCC(C)(C)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 106, 56, 56, 12, 56, 12, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 106, 160, 160, 201, 201, 201, 201, 201, 106, 56, 12, 12, 12, 12, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 10, 43, 13, 14, 15, 16, 17, 18, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 1087 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919558 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919558 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919558/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919558 Building REAL300004919559 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919559' /scratch/stefan/7775247/working/building/REAL300004919559 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919559 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919559/0 /scratch/stefan/7775247/working/building/REAL300004919559 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/562 `/scratch/stefan/7775247/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CC1=CC=CC=C1)NC(=O)C1=CC=CN=C1)C(=O)[O-]) `REAL300004919559.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919559 none CC#CCC(NC(=O)C(CC1=CC=CC=C1)NC(=O)C1=CC=CN=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 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: [63, 63, 63, 44, 21, 21, 7, 21, 2, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 31, 31, 31, 31, 31, 44, 47, 47, 63, 63, 63, 63, 63, 44, 21, 7, 2, 2, 1, 1, 1, 1, 1, 15, 31, 31, 31, 31] 104 rigid atoms, others: [38, 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, 43, 44, 45, 46, 47]) total number of confs: 341 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919559 none CC#CCC(NC(=O)C(CC1=CC=CC=C1)NC(=O)C1=CC=CN=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 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: [94, 94, 94, 79, 45, 45, 14, 45, 5, 14, 30, 31, 31, 31, 31, 31, 5, 1, 5, 1, 1, 1, 1, 1, 1, 79, 82, 82, 94, 94, 94, 94, 94, 79, 45, 14, 30, 30, 31, 31, 31, 31, 31, 5, 1, 1, 1, 1] 104 rigid atoms, others: [44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 475 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919559 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919559 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919559/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919559 Building REAL300004919560 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919560' /scratch/stefan/7775247/working/building/REAL300004919560 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919560 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919560/0 /scratch/stefan/7775247/working/building/REAL300004919560 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 563) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/563 `/scratch/stefan/7775247/working/3D/563' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CC=CO2)NC1=O)C(=O)[O-]) `REAL300004919560.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919560 none CC#CCC(NC(=O)C1=CC=C(C2=CC=CO2)NC1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 8, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 40, 13, 13, 1, 13, 1, 1, 1, 1, 1, 12, 12, 12, 12, 1, 1, 1, 40, 66, 66, 114, 114, 114, 114, 114, 40, 13, 1, 1, 12, 12, 12, 1] 201 rigid atoms, others: [35, 6, 8, 9, 10, 11, 12, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 560 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919560 none CC#CCC(NC(=O)C1=CC=C(C2=CC=CO2)NC1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 8, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 145, 85, 85, 12, 85, 12, 12, 12, 1, 1, 1, 1, 1, 1, 12, 12, 12, 145, 173, 173, 201, 201, 201, 201, 201, 145, 85, 12, 12, 1, 1, 1, 12] 201 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 877 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919560 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919560 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919560/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919560 Building REAL300004919561 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919561' /scratch/stefan/7775247/working/building/REAL300004919561 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919561 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919561/0 /scratch/stefan/7775247/working/building/REAL300004919561 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/564 `/scratch/stefan/7775247/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCC1=CC=C2CC3=CC=CC=C3C2=C1)C(=O)[O-]) `REAL300004919561.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919561 none CC#CCC(NC(=O)CCCC1=CC=C2CC3=CC=CC=C3C2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 128, 105, 55, 55, 11, 55, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 105, 105, 105, 128, 128, 128, 128, 128, 105, 55, 11, 11, 6, 6, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 128 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 559 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919561 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919561 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919561/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919561 Building REAL300004919562 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919562' /scratch/stefan/7775247/working/building/REAL300004919562 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919562 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919562/0 /scratch/stefan/7775247/working/building/REAL300004919562 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 565) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/565 `/scratch/stefan/7775247/working/3D/565' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=C(OC)C(OC)=C2)CCCC1)C(=O)[O-]) `REAL300004919562.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919562 none CC#CCC(NC(=O)C1(C2=CC=C(OC)C(OC)=C2)CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 21, 9, 9, 1, 9, 1, 1, 7, 7, 7, 7, 19, 7, 7, 19, 7, 1, 1, 1, 1, 21, 35, 35, 51, 51, 51, 51, 51, 21, 9, 7, 7, 19, 19, 19, 19, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [6, 8, 9, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 304 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: REAL300004919562 none CC#CCC(NC(=O)C1(C2=CC=C(OC)C(OC)=C2)CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 48, 23, 23, 7, 23, 1, 1, 1, 1, 1, 1, 3, 1, 1, 3, 1, 7, 7, 7, 7, 48, 75, 75, 100, 100, 100, 100, 100, 48, 23, 1, 1, 4, 4, 4, 4, 4, 4, 1, 7, 7, 7, 7, 7, 7, 7, 7] 201 rigid atoms, others: [33, 34, 8, 9, 10, 11, 12, 13, 15, 16, 18, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 546 number of broken/clashed sets: 157 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919562 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919562 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919562/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919562 Building REAL300004919563 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919563' /scratch/stefan/7775247/working/building/REAL300004919563 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919563 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919563/0 /scratch/stefan/7775247/working/building/REAL300004919563 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/566 `/scratch/stefan/7775247/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(N2CCOCC2)C=C1)C(=O)[O-]) `REAL300004919563.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919563 none CC#CCC(NC(=O)C=CC1=CC=C(N2CCOCC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 127, 60, 23, 23, 3, 23, 3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 1, 1, 60, 83, 83, 127, 127, 127, 127, 127, 60, 23, 3, 3, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1] 201 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 44, 20, 21, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 601 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919563 none CC#CCC(NC(=O)C=CC1=CC=C(N2CCOCC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 127, 82, 82, 18, 82, 18, 2, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 127, 155, 155, 201, 201, 201, 201, 201, 127, 82, 18, 18, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 201 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 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, 44, 45]) total number of confs: 913 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919563 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919563 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919563/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919563 Building REAL300004919564 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919564' /scratch/stefan/7775247/working/building/REAL300004919564 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919564 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919564/0 /scratch/stefan/7775247/working/building/REAL300004919564 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 567) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/567 `/scratch/stefan/7775247/working/3D/567' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C2CC2)=NC2=CC=C(C)C=C21)C(=O)[O-]) `REAL300004919564.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919564 none CC#CCC(NC(=O)C1=CC(C2CC2)=NC2=CC=C(C)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 32, 9, 9, 1, 9, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 32, 55, 55, 108, 108, 108, 108, 108, 32, 9, 1, 11, 11, 11, 11, 11, 1, 1, 2, 2, 2, 1] 201 rigid atoms, others: [32, 43, 38, 6, 39, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 529 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919564 none CC#CCC(NC(=O)C1=CC(C2CC2)=NC2=CC=C(C)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 115, 65, 65, 11, 65, 11, 11, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 115, 146, 146, 201, 201, 201, 201, 201, 115, 65, 11, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [33, 34, 35, 36, 37, 10, 11, 12, 13] 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, 38, 39, 40, 41, 42, 43]) total number of confs: 927 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919564 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919564 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919564/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919564 Building REAL300004919565 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919565' /scratch/stefan/7775247/working/building/REAL300004919565 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919565 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919565/0 /scratch/stefan/7775247/working/building/REAL300004919565 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/568 `/scratch/stefan/7775247/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CSC1=CC=CC(Br)=C1)C(=O)[O-]) `REAL300004919565.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919565 none CC#CCC(NC(=O)CSC1=CC=CC(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 120, 87, 87, 28, 87, 8, 1, 1, 1, 1, 1, 1, 1, 1, 120, 150, 150, 201, 201, 201, 201, 201, 120, 87, 28, 28, 1, 1, 1, 1] 201 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 969 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919565 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919565 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919565/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919565 Building REAL300004919566 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919566' /scratch/stefan/7775247/working/building/REAL300004919566 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919566 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919566/0 /scratch/stefan/7775247/working/building/REAL300004919566 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 569) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/569 `/scratch/stefan/7775247/working/3D/569' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(F)=CC2=CC=CN=C21)C(=O)[O-]) `REAL300004919566.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919566 none CC#CCC(NC(=O)C1=CC(F)=CC2=CC=CN=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 15, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 31, 12, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 48, 48, 78, 78, 78, 78, 78, 31, 13, 1, 1, 1, 1, 1] 78 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 390 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919566 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919566 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919566/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919566 Building REAL300004919567 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919567' /scratch/stefan/7775247/working/building/REAL300004919567 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919567 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919567/0 /scratch/stefan/7775247/working/building/REAL300004919567 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/570 `/scratch/stefan/7775247/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C([N+](=O)[O-])C2=CC=CN=C12)C(=O)[O-]) `REAL300004919567.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919567 none CC#CCC(NC(=O)C1=CC=C([N+](=O)[O-])C2=CC=CN=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 34, 12, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 34, 50, 50, 73, 73, 73, 73, 73, 34, 12, 1, 1, 1, 1, 1] 73 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 366 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919567 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919567 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919567/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919567 Building REAL300004919568 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919568' /scratch/stefan/7775247/working/building/REAL300004919568 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919568 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919568/0 /scratch/stefan/7775247/working/building/REAL300004919568 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 571) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/571 `/scratch/stefan/7775247/working/3D/571' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(COC2=CC=C(C)N=C2)=C1)C(=O)[O-]) `REAL300004919568.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919568 none CC#CCC(NC(=O)C1=CC=CC(COC2=CC=C(C)N=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 8, 15, 15, 15, 15, 15, 15, 1, 13, 19, 19, 33, 33, 33, 33, 33, 13, 5, 1, 1, 1, 8, 8, 15, 15, 15, 15, 15, 15, 1] 201 rigid atoms, others: [33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 44, 22] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919568 none CC#CCC(NC(=O)C1=CC=CC(COC2=CC=C(C)N=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 5, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 111, 55, 55, 15, 55, 15, 14, 15, 15, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 15, 111, 153, 153, 201, 201, 201, 201, 201, 111, 55, 14, 15, 15, 2, 2, 1, 1, 2, 2, 2, 1, 15] 201 rigid atoms, others: [38, 39, 43, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 44]) total number of confs: 1023 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919568 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919568 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919568/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919568 Building REAL300004919569 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919569' /scratch/stefan/7775247/working/building/REAL300004919569 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919569 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919569/0 /scratch/stefan/7775247/working/building/REAL300004919569 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/572 `/scratch/stefan/7775247/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)=CC1=CC=CC=C1Cl)C(=O)[O-]) `REAL300004919569.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919569 none CC#CCC(NC(=O)C(C)=CC1=CC=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 5, 1, 1, 1, 1, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [181, 181, 181, 89, 34, 34, 6, 34, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 89, 125, 125, 181, 181, 181, 181, 181, 89, 34, 6, 6, 6, 6, 1, 1, 1, 1] 181 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 875 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919569 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919569 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919569/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919569 Building REAL300004919570 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919570' /scratch/stefan/7775247/working/building/REAL300004919570 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919570 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919570/0 /scratch/stefan/7775247/working/building/REAL300004919570 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 573) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/573 `/scratch/stefan/7775247/working/3D/573' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)=CC1=CC=CC(Cl)=C1)C(=O)[O-]) `REAL300004919570.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919570 none CC#CCC(NC(=O)C(C)=CC1=CC=CC(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 5, 1, 1, 1, 1, 1, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 50, 50, 7, 50, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 118, 157, 157, 201, 201, 201, 201, 201, 118, 50, 7, 7, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 952 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919570 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919570 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919570/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919570 Building REAL300004919571 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919571' /scratch/stefan/7775247/working/building/REAL300004919571 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919571 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919571/0 /scratch/stefan/7775247/working/building/REAL300004919571 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/574 `/scratch/stefan/7775247/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1COC2=CC=C(F)C=C2C1)C(=O)[O-]) `REAL300004919571.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919571 none CC#CCC(NC(=O)C1COC2=CC=C(F)C=C2C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 44, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 61, 61, 86, 86, 86, 86, 86, 44, 13, 1, 1, 1, 1, 1, 1, 1, 1] 86 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 422 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919571 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919571 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919571/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919571 Building REAL300004919572 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919572' /scratch/stefan/7775247/working/building/REAL300004919572 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919572 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919572/0 /scratch/stefan/7775247/working/building/REAL300004919572 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 575) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/575 `/scratch/stefan/7775247/working/3D/575' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)OC(S(=O)(=O)NC)=C1)C(=O)[O-]) `REAL300004919572.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919572 none CC#CCC(NC(=O)C1=C(C)OC(S(=O)(=O)NC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 12, 1, 14, 11, 11, 8, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 6, 6, 4, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 24, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 6, 6, 6, 23, 1, 24, 43, 43, 71, 71, 71, 71, 71, 24, 9, 2, 2, 2, 23, 23, 23, 23, 1] 201 rigid atoms, others: [36, 6, 8, 9, 10, 11, 12, 13, 18] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 435 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919572 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919572 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919572/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919572 Building REAL300004919573 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919573' /scratch/stefan/7775247/working/building/REAL300004919573 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919573 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919573/0 /scratch/stefan/7775247/working/building/REAL300004919573 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/576 `/scratch/stefan/7775247/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CSC(C2CCCO2)=N1)C(=O)[O-]) `REAL300004919573.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919573 none CC#CCC(NC(=O)C1=CSC(C2CCCO2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 5, 5, 5, 5, 12, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 32, 11, 11, 1, 11, 1, 1, 1, 1, 1, 12, 12, 12, 12, 1, 32, 50, 50, 83, 83, 83, 83, 83, 32, 11, 1, 12, 12, 12, 12, 12, 12, 12] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 17, 28] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 413 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919573 none CC#CCC(NC(=O)C1=CSC(C2CCCO2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 5, 5, 5, 5, 12, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 125, 57, 57, 12, 57, 12, 12, 12, 1, 1, 1, 1, 1, 1, 12, 125, 161, 161, 201, 201, 201, 201, 201, 125, 57, 12, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 964 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919573 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919573 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919573/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919573 Building REAL300004919574 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919574' /scratch/stefan/7775247/working/building/REAL300004919574 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919574 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919574/0 /scratch/stefan/7775247/working/building/REAL300004919574 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 577) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/577 `/scratch/stefan/7775247/working/3D/577' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(C2=CC=CC=N2)=C1C)C(=O)[O-]) `REAL300004919574.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919574 none CC#CCC(NC(=O)C1=CC=CC(C2=CC=CC=N2)=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 39, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 39, 58, 58, 112, 112, 112, 112, 112, 39, 10, 1, 1, 1, 7, 7, 7, 7, 2, 2, 2] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919574 none CC#CCC(NC(=O)C1=CC=CC(C2=CC=CC=N2)=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 124, 53, 53, 7, 53, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 124, 156, 156, 201, 201, 201, 201, 201, 124, 53, 7, 7, 7, 1, 1, 1, 1, 7, 7, 7] 201 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40]) total number of confs: 924 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919574 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919574 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919574/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919574 Building REAL300004919575 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919575' /scratch/stefan/7775247/working/building/REAL300004919575 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919575 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919575/0 /scratch/stefan/7775247/working/building/REAL300004919575 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/578 `/scratch/stefan/7775247/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C2=CC=C(Cl)C(Cl)=C2)=NS1)C(=O)[O-]) `REAL300004919575.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919575 none CC#CCC(NC(=O)C1=CC(C2=CC=C(Cl)C(Cl)=C2)=NS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 16, 1, 16, 1, 8, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 7, 7, 1, 7, 1, 1, 1, 1, 12, 12, 2, 12, 12, 12, 12, 1, 1, 23, 35, 35, 46, 46, 46, 46, 46, 23, 7, 1, 12, 12, 12] 201 rigid atoms, others: [6, 8, 9, 10, 11, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919575 none CC#CCC(NC(=O)C1=CC(C2=CC=C(Cl)C(Cl)=C2)=NS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 16, 1, 16, 1, 8, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 64, 64, 12, 64, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 131, 157, 157, 201, 201, 201, 201, 201, 131, 64, 12, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 884 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919575 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919575 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919575/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919575 Building REAL300004919576 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919576' /scratch/stefan/7775247/working/building/REAL300004919576 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919576 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919576/0 /scratch/stefan/7775247/working/building/REAL300004919576 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 579) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/579 `/scratch/stefan/7775247/working/3D/579' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(CC)C(CC)=NNC1=O)C(=O)[O-]) `REAL300004919576.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919576 none CC#CCC(NC(=O)C1=C(CC)C(CC)=NNC1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 5, 5, 1, 5, 5, 8, 8, 1, 11, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 110, 39, 10, 10, 1, 10, 1, 1, 1, 3, 1, 1, 6, 1, 1, 1, 1, 39, 60, 60, 110, 110, 110, 110, 110, 39, 10, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 1] 201 rigid atoms, others: [6, 39, 8, 9, 10, 12, 13, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 7, 11, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 525 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919576 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919576 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919576/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919576 Building REAL300004919577 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919577' /scratch/stefan/7775247/working/building/REAL300004919577 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919577 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919577/0 /scratch/stefan/7775247/working/building/REAL300004919577 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/580 `/scratch/stefan/7775247/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(CCC(F)(F)F)C=C1)C(=O)[O-]) `REAL300004919577.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919577 none CC#CCC(NC(=O)C1=CC=C(CCC(F)(F)F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1, 14, 21, 21, 43, 43, 43, 43, 43, 14, 4, 1, 1, 8, 8, 8, 8, 1, 1] 99 rigid atoms, others: [36, 37, 6, 8, 9, 10, 11, 12, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919577 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919577 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919577/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919577 Building REAL300004919578 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919578' /scratch/stefan/7775247/working/building/REAL300004919578 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919578 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919578/0 /scratch/stefan/7775247/working/building/REAL300004919578 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 581) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/581 `/scratch/stefan/7775247/working/3D/581' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(F)C(OC)=C1)C(=O)[O-]) `REAL300004919578.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919578 none CC#CCC(NC(=O)C=CC1=CC=C(F)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [169, 169, 169, 82, 37, 37, 6, 37, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 82, 118, 118, 169, 169, 169, 169, 169, 82, 37, 6, 6, 1, 1, 4, 4, 4, 1] 201 rigid atoms, others: [32, 36, 9, 10, 11, 12, 13, 14, 15, 16, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 826 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919578 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919578 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919578/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919578 Building REAL300004919579 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919579' /scratch/stefan/7775247/working/building/REAL300004919579 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919579 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919579/0 /scratch/stefan/7775247/working/building/REAL300004919579 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/582 `/scratch/stefan/7775247/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)OC(C2=CC=C(OC)C=C2)=N1)C(=O)[O-]) `REAL300004919579.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919579 none CC#CCC(NC(=O)C1=C(C)OC(C2=CC=C(OC)C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 8, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 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: [95, 95, 95, 34, 11, 12, 1, 12, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 7, 3, 3, 1, 34, 55, 55, 95, 95, 95, 95, 95, 34, 12, 2, 2, 2, 3, 4, 6, 7, 7, 3, 3] 129 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 21] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 475 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: REAL300004919579 none CC#CCC(NC(=O)C1=C(C)OC(C2=CC=C(OC)C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 8, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 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: [110, 110, 110, 51, 23, 23, 3, 23, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 1, 1, 3, 51, 80, 80, 110, 110, 110, 110, 110, 51, 23, 4, 4, 4, 1, 1, 2, 2, 2, 1, 1] 129 rigid atoms, others: [35, 36, 40, 41, 12, 13, 14, 15, 16, 17, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39]) total number of confs: 573 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919579 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919579 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919579/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919579 Building REAL300004919580 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919580' /scratch/stefan/7775247/working/building/REAL300004919580 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919580 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919580/0 /scratch/stefan/7775247/working/building/REAL300004919580 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 583) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/583 `/scratch/stefan/7775247/working/3D/583' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN=C2SC(C)=C(C)N2C1=O)C(=O)[O-]) `REAL300004919580.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919580 none CC#CCC(NC(=O)C1=CN=C2SC(C)=C(C)N2C1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 14, 1, 5, 1, 5, 8, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 2, 2, 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: [83, 83, 83, 43, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 59, 59, 83, 83, 83, 83, 83, 43, 13, 1, 2, 2, 2, 2, 2, 2] 83 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 412 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919580 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919580 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919580/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919580 Building REAL300004919581 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919581' /scratch/stefan/7775247/working/building/REAL300004919581 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919581 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919581/0 /scratch/stefan/7775247/working/building/REAL300004919581 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/584 `/scratch/stefan/7775247/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(CC(C)C)N=C(C)S1)C(=O)[O-]) `REAL300004919581.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919581 none CC#CCC(NC(=O)C1=C(CC(C)C)N=C(C)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 5, 5, 5, 8, 1, 5, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 42, 9, 9, 1, 9, 1, 1, 1, 5, 9, 10, 1, 1, 1, 1, 42, 66, 66, 114, 114, 114, 114, 114, 42, 10, 5, 5, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2] 201 rigid atoms, others: [6, 8, 9, 10, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 588 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919581 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919581 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919581/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919581 Building REAL300004919582 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919582' /scratch/stefan/7775247/working/building/REAL300004919582 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919582 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919582/0 /scratch/stefan/7775247/working/building/REAL300004919582 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 585) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/585 `/scratch/stefan/7775247/working/3D/585' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(Br)=C1Cl)C(=O)[O-]) `REAL300004919582.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919582 none CC#CCC(NC(=O)C1=CC=CC(Br)=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 17, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 23, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 23, 33, 33, 60, 60, 60, 60, 60, 23, 7, 1, 1, 1] 60 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919582 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919582 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919582/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919582 Building REAL300004919583 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919583' /scratch/stefan/7775247/working/building/REAL300004919583 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919583 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919583/0 /scratch/stefan/7775247/working/building/REAL300004919583 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/586 `/scratch/stefan/7775247/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N=C(C2=CC=CC=C2)O1)C(=O)[O-]) `REAL300004919583.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919583 none CC#CCC(NC(=O)C1=C(C)N=C(C2=CC=CC=C2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 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: [79, 79, 79, 36, 11, 12, 1, 12, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 36, 54, 54, 79, 79, 79, 79, 79, 36, 12, 2, 2, 2, 3, 3, 2, 3, 3] 81 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 19] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 407 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: REAL300004919583 none CC#CCC(NC(=O)C1=C(C)N=C(C2=CC=CC=C2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 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, 56, 26, 26, 3, 26, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 56, 68, 68, 81, 81, 81, 81, 81, 56, 26, 4, 4, 4, 1, 1, 1, 1, 1] 81 rigid atoms, others: [33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 368 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919583 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919583 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919583/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919583 Building REAL300004919584 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919584' /scratch/stefan/7775247/working/building/REAL300004919584 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919584 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919584/0 /scratch/stefan/7775247/working/building/REAL300004919584 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 587) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/587 `/scratch/stefan/7775247/working/3D/587' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(NC(=O)C(C)(C)C)=CC=C1F)C(=O)[O-]) `REAL300004919584.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919584 none CC#CCC(NC(=O)C1=CC(NC(=O)C(C)(C)C)=CC=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 31, 12, 12, 1, 12, 1, 1, 1, 1, 8, 8, 8, 13, 13, 13, 1, 1, 1, 1, 31, 50, 50, 86, 86, 86, 86, 86, 31, 12, 1, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1] 201 rigid atoms, others: [32, 43, 6, 8, 9, 10, 11, 44, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 456 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919584 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919584 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919584/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919584 Building REAL300004919585 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919585' /scratch/stefan/7775247/working/building/REAL300004919585 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919585 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919585/0 /scratch/stefan/7775247/working/building/REAL300004919585 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/588 `/scratch/stefan/7775247/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)C1=CC=C(Br)C=C1)C(=O)[O-]) `REAL300004919585.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919585 none CC#CCC(NC(=O)C(C)C1=CC=C(Br)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [175, 175, 175, 66, 25, 25, 4, 25, 1, 4, 1, 1, 1, 1, 1, 1, 1, 66, 100, 100, 175, 175, 175, 175, 175, 66, 25, 4, 4, 4, 4, 1, 1, 1, 1] 175 rigid atoms, others: [32, 33, 34, 8, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 824 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919585 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919585 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919585/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919585 Building REAL300004919586 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919586' /scratch/stefan/7775247/working/building/REAL300004919586 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919586 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919586/0 /scratch/stefan/7775247/working/building/REAL300004919586 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 589) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/589 `/scratch/stefan/7775247/working/3D/589' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(CC(=O)NC2CCCCC2)N=C1)C(=O)[O-]) `REAL300004919586.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919586 none CC#CCC(NC(=O)C1=CN(CC(=O)NC2CCCCC2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 5, 5, 1, 5, 1, 1, 1, 1, 7, 18, 18, 18, 32, 32, 32, 32, 32, 1, 1, 11, 17, 17, 28, 28, 28, 28, 28, 11, 5, 1, 7, 7, 18, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1] 201 rigid atoms, others: [33, 6, 8, 9, 10, 11, 48, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919586 none CC#CCC(NC(=O)C1=CN(CC(=O)NC2CCCCC2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 124, 70, 70, 32, 70, 32, 32, 13, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 32, 32, 124, 150, 150, 201, 201, 201, 201, 201, 124, 70, 32, 13, 13, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 46, 47] 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, 48]) total number of confs: 948 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919586 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919586 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919586/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919586 Building REAL300004919587 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919587' /scratch/stefan/7775247/working/building/REAL300004919587 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919587 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919587/0 /scratch/stefan/7775247/working/building/REAL300004919587 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/590 `/scratch/stefan/7775247/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C2CC2)=NC2=CC=C(F)C=C21)C(=O)[O-]) `REAL300004919587.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919587 none CC#CCC(NC(=O)C1=CC(C2CC2)=NC2=CC=C(F)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 30, 9, 9, 1, 9, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 30, 52, 52, 100, 100, 100, 100, 100, 30, 9, 1, 11, 11, 11, 11, 11, 1, 1, 1] 201 rigid atoms, others: [32, 38, 6, 39, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 40] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 492 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919587 none CC#CCC(NC(=O)C1=CC(C2CC2)=NC2=CC=C(F)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 120, 65, 65, 11, 65, 11, 11, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 120, 151, 151, 201, 201, 201, 201, 201, 120, 65, 11, 1, 1, 1, 1, 1, 11, 11, 11] 201 rigid atoms, others: [33, 34, 35, 36, 37, 10, 11, 12, 13] 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, 38, 39, 40]) total number of confs: 927 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919587 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919587 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919587/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919587 Building REAL300004919588 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919588' /scratch/stefan/7775247/working/building/REAL300004919588 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919588 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919588/0 /scratch/stefan/7775247/working/building/REAL300004919588 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 591) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/591 `/scratch/stefan/7775247/working/3D/591' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1CCC(C(C)(C)C)CC1)C(=O)[O-]) `REAL300004919588.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919588 none CC#CCC(NC(=O)CC1CCC(C(C)(C)C)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [197, 197, 197, 95, 36, 36, 7, 36, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 95, 133, 133, 197, 197, 197, 197, 197, 95, 36, 7, 7, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 49, 8, 9, 10, 11, 12, 13, 46, 47, 48, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 953 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919588 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919588 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919588/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919588 Building REAL300004919589 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919589' /scratch/stefan/7775247/working/building/REAL300004919589 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919589 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919589/0 /scratch/stefan/7775247/working/building/REAL300004919589 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/592 `/scratch/stefan/7775247/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)CCCC1=CC=CC=C1)C(=O)[O-]) `REAL300004919589.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919589 none CC#CCC(NC(=O)C(C)CCCC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 134, 70, 70, 20, 70, 8, 20, 7, 4, 1, 1, 1, 1, 1, 1, 1, 134, 179, 179, 201, 201, 201, 201, 201, 134, 70, 20, 20, 20, 20, 8, 8, 7, 7, 4, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 1074 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919589 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919589 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919589/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919589 Building REAL300004919590 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919590' /scratch/stefan/7775247/working/building/REAL300004919590 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919590 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919590/0 /scratch/stefan/7775247/working/building/REAL300004919590 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 593) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/593 `/scratch/stefan/7775247/working/3D/593' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)CC1=CC=CC(Cl)=C1)C(=O)[O-]) `REAL300004919590.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919590 none CC#CCC(NC(=O)C(C)CC1=CC=CC(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 16, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 104, 49, 49, 10, 49, 3, 10, 1, 1, 1, 1, 1, 1, 1, 1, 104, 137, 137, 201, 201, 201, 201, 201, 104, 49, 10, 10, 10, 10, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 963 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919590 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919590 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919590/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919590 Building REAL300004919591 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919591' /scratch/stefan/7775247/working/building/REAL300004919591 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919591 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919591/0 /scratch/stefan/7775247/working/building/REAL300004919591 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/594 `/scratch/stefan/7775247/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C2NC(=O)N(C)C2=C1)C(=O)[O-]) `REAL300004919591.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919591 none CC#CCC(NC(=O)C1=CC=C2NC(=O)N(C)C2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 8, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 29, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 40, 40, 73, 73, 73, 73, 73, 29, 7, 1, 1, 1, 2, 2, 2, 1] 73 rigid atoms, others: [35, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 32, 34, 33, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 329 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919591 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919591 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919591/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919591 Building REAL300004919592 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919592' /scratch/stefan/7775247/working/building/REAL300004919592 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919592 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919592/0 /scratch/stefan/7775247/working/building/REAL300004919592 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 595) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/595 `/scratch/stefan/7775247/working/3D/595' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(=O)NC(CC(C)C)=C1)C(=O)[O-]) `REAL300004919592.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919592 none CC#CCC(NC(=O)C1=CC(=O)NC(CC(C)C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 11, 8, 1, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 19, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 19, 29, 29, 69, 69, 69, 69, 69, 19, 6, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 1] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 40, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 344 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919592 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919592 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919592/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919592 Building REAL300004919593 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919593' /scratch/stefan/7775247/working/building/REAL300004919593 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919593 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919593/0 /scratch/stefan/7775247/working/building/REAL300004919593 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/596 `/scratch/stefan/7775247/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C(=O)NC2CC2)C=C1)C(=O)[O-]) `REAL300004919593.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919593 none CC#CCC(NC(=O)C1=CC=C(C(=O)NC2CC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 7, 7, 7, 28, 28, 1, 1, 15, 24, 24, 58, 58, 58, 58, 58, 15, 4, 1, 1, 7, 28, 28, 28, 28, 28, 1, 1] 201 rigid atoms, others: [38, 6, 39, 8, 9, 10, 11, 12, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 317 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919593 none CC#CCC(NC(=O)C1=CC=C(C(=O)NC2CC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 58, 58, 28, 58, 28, 28, 28, 6, 6, 6, 1, 1, 1, 1, 28, 28, 118, 149, 149, 201, 201, 201, 201, 201, 118, 58, 28, 28, 6, 1, 1, 1, 1, 1, 28, 28] 201 rigid atoms, others: [33, 34, 35, 36, 37, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39]) total number of confs: 946 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919593 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919593 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919593/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919593 Building REAL300004919594 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919594' /scratch/stefan/7775247/working/building/REAL300004919594 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919594 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919594/0 /scratch/stefan/7775247/working/building/REAL300004919594 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 597) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/597 `/scratch/stefan/7775247/working/3D/597' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(NS(C)(=O)=O)C(C)(C)C)C(=O)[O-]) `REAL300004919594.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.0.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.0.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.0.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919594 none CC#CCC(NC(=O)C(NS(C)(=O)=O)C(C)(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 8, 14, 5, 11, 11, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 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: [11, 11, 11, 6, 4, 4, 1, 4, 1, 1, 2, 4, 4, 4, 1, 2, 2, 2, 6, 7, 7, 11, 11, 11, 11, 11, 6, 4, 1, 2, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2] 12 rigid atoms, others: [8, 9, 28, 14, 6] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 65 number of broken/clashed sets: 0 ./output.0.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919594 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919594 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919594/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919594 Building REAL300004919595 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919595' /scratch/stefan/7775247/working/building/REAL300004919595 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919595 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919595/0 /scratch/stefan/7775247/working/building/REAL300004919595 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/598 `/scratch/stefan/7775247/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C2=CC=CC=N2)=CC=C1Cl)C(=O)[O-]) `REAL300004919595.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919595 none CC#CCC(NC(=O)C1=CC(C2=CC=CC=N2)=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 24, 7, 7, 1, 7, 1, 1, 1, 1, 11, 11, 11, 11, 11, 1, 1, 1, 1, 24, 40, 40, 70, 70, 70, 70, 70, 24, 7, 1, 11, 11, 11, 11, 1, 1] 201 rigid atoms, others: [36, 37, 6, 8, 9, 10, 11, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35]) total number of confs: 348 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919595 none CC#CCC(NC(=O)C1=CC(C2=CC=CC=N2)=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 108, 51, 51, 11, 51, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 108, 144, 144, 201, 201, 201, 201, 201, 108, 51, 11, 1, 1, 1, 1, 11, 11] 201 rigid atoms, others: [32, 33, 34, 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, 36, 37]) total number of confs: 949 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919595 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919595 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919595/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919595 Building REAL300004919596 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919596' /scratch/stefan/7775247/working/building/REAL300004919596 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919596 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919596/0 /scratch/stefan/7775247/working/building/REAL300004919596 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 599) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/599 `/scratch/stefan/7775247/working/3D/599' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=NC(OC2CCC2)=C1)C(=O)[O-]) `REAL300004919596.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919596 none CC#CCC(NC(=O)C1=CC=NC(OC2CCC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 8, 1, 12, 5, 5, 5, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 10, 24, 24, 24, 1, 17, 28, 28, 55, 55, 55, 55, 55, 17, 5, 1, 1, 24, 24, 24, 24, 24, 24, 24, 1] 201 rigid atoms, others: [38, 6, 8, 9, 10, 11, 12, 13, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 308 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919596 none CC#CCC(NC(=O)C1=CC=NC(OC2CCC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 8, 1, 12, 5, 5, 5, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 59, 59, 24, 59, 24, 24, 24, 24, 6, 1, 1, 1, 1, 1, 24, 118, 145, 145, 201, 201, 201, 201, 201, 118, 59, 24, 24, 1, 1, 1, 1, 1, 1, 1, 24] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38]) total number of confs: 893 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919596 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919596 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919596/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919596 Building REAL300004919597 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919597' /scratch/stefan/7775247/working/building/REAL300004919597 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919597 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919597/0 /scratch/stefan/7775247/working/building/REAL300004919597 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/600 `/scratch/stefan/7775247/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC)C(N2C=NN=N2)=C1)C(=O)[O-]) `REAL300004919597.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919597 none CC#CCC(NC(=O)C1=CC=C(OC)C(N2C=NN=N2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 8, 1, 8, 8, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 4, 1, 1, 6, 6, 6, 6, 1, 17, 32, 32, 67, 67, 67, 67, 67, 17, 5, 1, 1, 4, 4, 4, 6, 1] 201 rigid atoms, others: [32, 37, 6, 8, 9, 10, 11, 12, 14, 15, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36]) total number of confs: 318 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919597 none CC#CCC(NC(=O)C1=CC=C(OC)C(N2C=NN=N2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 8, 1, 8, 8, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [156, 156, 156, 63, 21, 21, 6, 21, 6, 5, 6, 6, 6, 13, 1, 1, 1, 1, 1, 1, 6, 63, 101, 101, 156, 156, 156, 156, 156, 63, 21, 5, 6, 13, 13, 13, 1, 6] 201 rigid atoms, others: [36, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37]) total number of confs: 784 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919597 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919597 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919597/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919597 Building REAL300004919598 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919598' /scratch/stefan/7775247/working/building/REAL300004919598 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919598 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919598/0 /scratch/stefan/7775247/working/building/REAL300004919598 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 601) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/601 `/scratch/stefan/7775247/working/3D/601' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=COC(C2=CC=C(Br)C=C2F)=N1)C(=O)[O-]) `REAL300004919598.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919598 none CC#CCC(NC(=O)C1=COC(C2=CC=C(Br)C=C2F)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 1, 1, 1, 17, 1, 1, 15, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [82, 82, 82, 34, 12, 12, 1, 12, 1, 1, 1, 1, 1, 12, 12, 1, 12, 12, 12, 12, 1, 34, 52, 52, 82, 82, 82, 82, 82, 34, 12, 1, 12, 12, 12] 174 rigid atoms, others: [6, 8, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34]) total number of confs: 419 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919598 none CC#CCC(NC(=O)C1=COC(C2=CC=C(Br)C=C2F)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 1, 1, 1, 17, 1, 1, 15, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [174, 174, 174, 114, 57, 57, 12, 57, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 114, 135, 135, 174, 174, 174, 174, 174, 114, 57, 12, 1, 1, 1] 174 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 769 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919598 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919598 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919598/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919598 Building REAL300004919599 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919599' /scratch/stefan/7775247/working/building/REAL300004919599 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919599 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919599/0 /scratch/stefan/7775247/working/building/REAL300004919599 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/602 `/scratch/stefan/7775247/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC2=C(C=CC3=C2C=CC=C3)O1)C(=O)[O-]) `REAL300004919599.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919599 none CC#CCC(NC(=O)CC1=CC2=C(C=CC3=C2C=CC=C3)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 109, 56, 55, 8, 55, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 109, 148, 148, 201, 201, 201, 201, 201, 109, 55, 8, 8, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 33, 32, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 998 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919599 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919599 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919599/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919599 Building REAL300004919600 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919600' /scratch/stefan/7775247/working/building/REAL300004919600 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919600 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919600/0 /scratch/stefan/7775247/working/building/REAL300004919600 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 603) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/603 `/scratch/stefan/7775247/working/3D/603' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CC(=O)N(C2=CC=C(F)C(C)=C2)C1)C(=O)[O-]) `REAL300004919600.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919600 none CC#CCC(NC(=O)C1CC(=O)N(C2=CC=C(F)C(C)=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 5, 1, 11, 8, 1, 1, 1, 1, 15, 1, 5, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 31, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 10, 10, 2, 9, 10, 10, 10, 1, 31, 48, 48, 66, 66, 66, 66, 66, 31, 10, 1, 1, 1, 10, 10, 10, 10, 10, 10, 1, 1] 201 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 21, 41, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 354 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: REAL300004919600 none CC#CCC(NC(=O)C1CC(=O)N(C2=CC=C(F)C(C)=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 5, 1, 11, 8, 1, 1, 1, 1, 15, 1, 5, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 110, 50, 50, 10, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 110, 146, 146, 201, 201, 201, 201, 201, 110, 50, 10, 10, 10, 1, 1, 2, 2, 2, 1, 10, 10] 201 rigid atoms, others: [35, 36, 40, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 41, 42]) total number of confs: 943 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919600 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919600 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919600/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919600 Building REAL300004919601 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919601' /scratch/stefan/7775247/working/building/REAL300004919601 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919601 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919601/0 /scratch/stefan/7775247/working/building/REAL300004919601 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/604 `/scratch/stefan/7775247/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CC(=O)N(C)C1C1=CC=C(Cl)C(F)=C1)C(=O)[O-]) `REAL300004919601.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919601 none CC#CCC(NC(=O)C1CC(=O)N(C)C1C1=CC=C(Cl)C(F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 16, 1, 15, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 98, 98, 39, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 4, 4, 5, 5, 5, 39, 65, 65, 98, 98, 98, 98, 98, 39, 11, 1, 1, 1, 2, 2, 2, 1, 5, 5, 5] 193 rigid atoms, others: [33, 34, 35, 6, 39, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 40, 41, 42]) total number of confs: 504 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: REAL300004919601 none CC#CCC(NC(=O)C1CC(=O)N(C)C1C1=CC=C(Cl)C(F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 1, 1, 1, 1, 16, 1, 15, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [193, 193, 193, 100, 34, 34, 5, 34, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 100, 136, 136, 193, 193, 193, 193, 193, 100, 34, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1] 193 rigid atoms, others: [40, 41, 42, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 920 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919601 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919601 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919601/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919601 Building REAL300004919602 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919602' /scratch/stefan/7775247/working/building/REAL300004919602 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919602 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919602/0 /scratch/stefan/7775247/working/building/REAL300004919602 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 605) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/605 `/scratch/stefan/7775247/working/3D/605' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(F)(F)C1=CC=CC=C1OCC)C(=O)[O-]) `REAL300004919602.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919602 none CC#CCC(NC(=O)C(F)(F)C1=CC=CC=C1OCC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 15, 15, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [140, 140, 140, 69, 38, 38, 10, 38, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 7, 20, 69, 99, 99, 140, 140, 140, 140, 140, 69, 38, 1, 1, 1, 1, 20, 20, 21, 21, 21] 201 rigid atoms, others: [32, 33, 8, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38]) total number of confs: 763 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919602 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919602 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919602/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919602 Building REAL300004919603 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919603' /scratch/stefan/7775247/working/building/REAL300004919603 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919603 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919603/0 /scratch/stefan/7775247/working/building/REAL300004919603 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/606 `/scratch/stefan/7775247/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC([N+](=O)[O-])=CC=C1SC1CCCC1)C(=O)[O-]) `REAL300004919603.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919603 none CC#CCC(NC(=O)C1=CC([N+](=O)[O-])=CC=C1SC1CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 8, 11, 11, 1, 1, 1, 14, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 27, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 23, 23, 23, 23, 27, 40, 40, 74, 74, 74, 74, 74, 27, 10, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23] 201 rigid atoms, others: [33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44]) 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: REAL300004919603 none CC#CCC(NC(=O)C1=CC([N+](=O)[O-])=CC=C1SC1CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 8, 11, 11, 1, 1, 1, 14, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 74, 74, 23, 74, 23, 23, 21, 23, 23, 23, 23, 23, 7, 1, 1, 1, 1, 1, 1, 119, 153, 153, 201, 201, 201, 201, 201, 119, 74, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 933 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919603 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919603 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919603/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919603 Building REAL300004919604 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919604' /scratch/stefan/7775247/working/building/REAL300004919604 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919604 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919604/0 /scratch/stefan/7775247/working/building/REAL300004919604 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 607) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/607 `/scratch/stefan/7775247/working/3D/607' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(OC2=CC=C(Cl)C=C2)=N1)C(=O)[O-]) `REAL300004919604.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919604 none CC#CCC(NC(=O)C1=CC=CC(OC2=CC=C(Cl)C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 8, 20, 20, 12, 20, 20, 20, 1, 14, 24, 24, 49, 49, 49, 49, 49, 14, 5, 1, 1, 1, 20, 20, 20, 20] 201 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 21] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919604 none CC#CCC(NC(=O)C1=CC=CC(OC2=CC=C(Cl)C=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 102, 47, 47, 20, 47, 20, 20, 20, 20, 5, 1, 1, 1, 1, 1, 1, 1, 1, 20, 102, 137, 137, 201, 201, 201, 201, 201, 102, 47, 20, 20, 20, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 962 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919604 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919604 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919604/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919604 Building REAL300004919605 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919605' /scratch/stefan/7775247/working/building/REAL300004919605 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919605 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919605/0 /scratch/stefan/7775247/working/building/REAL300004919605 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/608 `/scratch/stefan/7775247/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=C(C)N(CC(F)(F)F)N=C1C)C(=O)[O-]) `REAL300004919605.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919605 none CC#CCC(NC(=O)CC1=C(C)N(CC(F)(F)F)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 1, 1, 5, 8, 5, 5, 15, 15, 15, 8, 1, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 55, 25, 24, 6, 25, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 55, 84, 84, 114, 114, 114, 114, 114, 55, 24, 6, 6, 2, 2, 2, 5, 5, 2, 2, 2] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 619 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919605 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919605 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919605/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919605 Building REAL300004919606 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919606' /scratch/stefan/7775247/working/building/REAL300004919606 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919606 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919606/0 /scratch/stefan/7775247/working/building/REAL300004919606 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 609) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/609 `/scratch/stefan/7775247/working/3D/609' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(C2=CC=CC=C2OCC)=C1)C(=O)[O-]) `REAL300004919606.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919606 none CC#CCC(NC(=O)C1=CC=CC(C2=CC=CC=C2OCC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 4, 7, 7, 7, 20, 34, 1, 13, 20, 20, 35, 35, 35, 35, 35, 13, 5, 1, 1, 1, 7, 7, 7, 7, 34, 34, 34, 34, 34, 1] 201 rigid atoms, others: [33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 45, 22] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 281 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919606 none CC#CCC(NC(=O)C1=CC=CC(C2=CC=CC=C2OCC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [150, 150, 150, 67, 25, 25, 7, 25, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 18, 7, 67, 99, 99, 150, 150, 150, 150, 150, 67, 25, 7, 7, 7, 1, 1, 1, 1, 18, 18, 18, 18, 18, 7] 201 rigid atoms, others: [36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45]) total number of confs: 782 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919606 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919606 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919606/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919606 Building REAL300004919607 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919607' /scratch/stefan/7775247/working/building/REAL300004919607 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919607 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919607/0 /scratch/stefan/7775247/working/building/REAL300004919607 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/610 `/scratch/stefan/7775247/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=NC(C3CC3)=NO2)C=C1)C(=O)[O-]) `REAL300004919607.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919607 none CC#CCC(NC(=O)C1=CC=C(C2=NC(C3CC3)=NO2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 12, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 4, 4, 4, 42, 42, 4, 4, 1, 1, 11, 21, 21, 54, 54, 54, 54, 54, 11, 4, 1, 1, 43, 42, 42, 43, 43, 1, 1] 201 rigid atoms, others: [32, 33, 6, 39, 8, 9, 10, 11, 12, 40, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 328 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919607 none CC#CCC(NC(=O)C1=CC=C(C2=NC(C3CC3)=NO2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 12, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 78, 78, 12, 78, 12, 42, 42, 12, 12, 12, 1, 1, 1, 1, 12, 12, 42, 43, 131, 152, 152, 201, 201, 201, 201, 201, 131, 78, 43, 43, 1, 1, 1, 1, 1, 43, 43] 201 rigid atoms, others: [34, 35, 36, 37, 38, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40]) total number of confs: 951 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919607 none CC#CCC(NC(=O)C1=CC=C(C2=NC(C3CC3)=NO2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 5, 5, 5, 8, 12, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 113, 34, 12, 12, 1, 12, 1, 4, 4, 1, 1, 1, 1, 1, 12, 12, 1, 1, 4, 4, 34, 59, 59, 113, 113, 113, 113, 113, 34, 12, 5, 5, 12, 12, 12, 12, 12, 5, 5] 201 rigid atoms, others: [11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 577 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919607 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919607 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919607/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919607 Building REAL300004919608 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919608' /scratch/stefan/7775247/working/building/REAL300004919608 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919608 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919608/0 /scratch/stefan/7775247/working/building/REAL300004919608 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 611) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/611 `/scratch/stefan/7775247/working/3D/611' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C)C=C1SC1=CC=CC=C1)C(=O)[O-]) `REAL300004919608.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919608 none CC#CCC(NC(=O)C1=CC=C(C)C=C1SC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 27, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 9, 22, 22, 9, 22, 22, 27, 40, 40, 73, 73, 73, 73, 73, 27, 10, 1, 1, 2, 2, 2, 1, 22, 22, 11, 22, 22] 201 rigid atoms, others: [32, 33, 37, 6, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 391 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919608 none CC#CCC(NC(=O)C1=CC=C(C)C=C1SC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 121, 72, 76, 22, 76, 22, 22, 22, 22, 22, 22, 6, 1, 1, 1, 1, 1, 1, 1, 121, 149, 149, 201, 201, 201, 201, 201, 121, 76, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 891 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919608 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919608 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919608/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919608 Building REAL300004919609 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919609' /scratch/stefan/7775247/working/building/REAL300004919609 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919609 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919609/0 /scratch/stefan/7775247/working/building/REAL300004919609 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/612 `/scratch/stefan/7775247/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=NC(OC2CCOC2)=C1)C(=O)[O-]) `REAL300004919609.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919609 none CC#CCC(NC(=O)C1=CC=NC(OC2CCOC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 8, 1, 12, 5, 5, 5, 12, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 21, 21, 21, 21, 1, 17, 29, 29, 54, 54, 54, 54, 54, 17, 5, 1, 1, 21, 21, 21, 21, 21, 21, 21, 1] 201 rigid atoms, others: [6, 39, 8, 9, 10, 11, 12, 13, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) 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: REAL300004919609 none CC#CCC(NC(=O)C1=CC=NC(OC2CCOC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 8, 1, 12, 5, 5, 5, 12, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 120, 61, 61, 21, 61, 21, 21, 21, 21, 6, 1, 1, 1, 1, 1, 1, 21, 120, 148, 148, 201, 201, 201, 201, 201, 120, 61, 21, 21, 1, 1, 1, 1, 1, 1, 1, 21] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39]) total number of confs: 911 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919609 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919609 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919609/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919609 Building REAL300004919610 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919610' /scratch/stefan/7775247/working/building/REAL300004919610 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919610 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919610/0 /scratch/stefan/7775247/working/building/REAL300004919610 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 613) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/613 `/scratch/stefan/7775247/working/3D/613' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C)=CC=C1SC1CCCC1)C(=O)[O-]) `REAL300004919610.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919610 none CC#CCC(NC(=O)C1=CC(C)=CC=C1SC1CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 5, 1, 1, 1, 14, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 25, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 9, 22, 22, 22, 22, 25, 38, 38, 67, 67, 67, 67, 67, 25, 11, 1, 2, 2, 2, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22] 201 rigid atoms, others: [35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 362 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: REAL300004919610 none CC#CCC(NC(=O)C1=CC(C)=CC=C1SC1CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 5, 1, 1, 1, 14, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 108, 73, 73, 22, 73, 22, 22, 20, 22, 22, 22, 7, 1, 1, 1, 1, 1, 1, 108, 144, 144, 201, 201, 201, 201, 201, 108, 73, 22, 22, 22, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 910 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919610 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919610 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919610/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919610 Building REAL300004919611 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919611' /scratch/stefan/7775247/working/building/REAL300004919611 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919611 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919611/0 /scratch/stefan/7775247/working/building/REAL300004919611 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/614 `/scratch/stefan/7775247/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C(=O)NC2=CC=CC=C2)C=C1)C(=O)[O-]) `REAL300004919611.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919611 none CC#CCC(NC(=O)C1=CC=C(C(=O)NC2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 7, 7, 7, 24, 24, 7, 24, 24, 1, 1, 16, 26, 26, 59, 59, 59, 59, 59, 16, 4, 1, 1, 7, 24, 24, 7, 24, 24, 1, 1] 188 rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 12, 21, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 325 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919611 none CC#CCC(NC(=O)C1=CC=C(C(=O)NC2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [182, 182, 182, 99, 37, 37, 5, 37, 5, 24, 24, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 24, 24, 99, 128, 127, 182, 182, 182, 182, 182, 99, 37, 24, 24, 5, 1, 1, 1, 1, 1, 24, 24] 188 rigid atoms, others: [36, 37, 38, 39, 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, 41, 42]) total number of confs: 879 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919611 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919611 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919611/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919611 Building REAL300004919612 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919612' /scratch/stefan/7775247/working/building/REAL300004919612 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919612 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919612/0 /scratch/stefan/7775247/working/building/REAL300004919612 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 615) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/615 `/scratch/stefan/7775247/working/3D/615' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C2CC2)=NC2=CC=C(OC)C=C21)C(=O)[O-]) `REAL300004919612.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919612 none CC#CCC(NC(=O)C1=CC(C2CC2)=NC2=CC=C(OC)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 27, 9, 9, 1, 9, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 2, 1, 1, 27, 48, 48, 82, 82, 82, 82, 82, 27, 9, 1, 11, 11, 11, 11, 11, 1, 1, 3, 3, 3, 1] 201 rigid atoms, others: [33, 6, 39, 8, 9, 10, 11, 44, 14, 15, 16, 17, 18, 19, 21, 22, 40] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 41, 42, 43]) total number of confs: 430 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919612 none CC#CCC(NC(=O)C1=CC(C2CC2)=NC2=CC=C(OC)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [176, 176, 176, 100, 58, 58, 11, 58, 11, 11, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 19, 11, 11, 100, 131, 131, 176, 176, 176, 176, 176, 100, 58, 11, 1, 1, 1, 1, 1, 11, 11, 19, 19, 19, 11] 201 rigid atoms, others: [34, 35, 36, 37, 38, 10, 11, 12, 13] 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, 39, 40, 41, 42, 43, 44]) total number of confs: 822 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919612 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919612 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919612/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919612 Building REAL300004919613 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919613' /scratch/stefan/7775247/working/building/REAL300004919613 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919613 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919613/0 /scratch/stefan/7775247/working/building/REAL300004919613 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/616 `/scratch/stefan/7775247/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2F)C(=O)C=C1)C(=O)[O-]) `REAL300004919613.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919613 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2F)C(=O)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 11, 11, 1, 11, 1, 1, 1, 1, 9, 9, 1, 9, 9, 9, 1, 1, 1, 1, 35, 52, 52, 79, 79, 79, 79, 79, 35, 11, 9, 9, 8, 9, 1, 1] 201 rigid atoms, others: [36, 37, 6, 8, 9, 10, 11, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 415 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919613 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2F)C(=O)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 15, 1, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 109, 51, 51, 9, 51, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 109, 151, 151, 201, 201, 201, 201, 201, 109, 51, 1, 1, 1, 1, 9, 9] 201 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37]) total number of confs: 993 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919613 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919613 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919613/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919613 Building REAL300004919614 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919614' /scratch/stefan/7775247/working/building/REAL300004919614 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919614 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919614/0 /scratch/stefan/7775247/working/building/REAL300004919614 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 617) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/617 `/scratch/stefan/7775247/working/3D/617' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=NC(OC2CCCCC2)=C1)C(=O)[O-]) `REAL300004919614.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919614 none CC#CCC(NC(=O)C1=CC=NC(OC2CCCCC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 8, 1, 12, 5, 5, 5, 5, 5, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 17, 17, 17, 17, 17, 1, 15, 26, 26, 51, 51, 51, 51, 51, 15, 5, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 44, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 280 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919614 none CC#CCC(NC(=O)C1=CC=NC(OC2CCCCC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 8, 1, 12, 5, 5, 5, 5, 5, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 108, 54, 54, 17, 54, 17, 17, 17, 17, 5, 1, 1, 1, 1, 1, 1, 1, 17, 108, 141, 141, 201, 201, 201, 201, 201, 108, 54, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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, 44]) total number of confs: 954 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919614 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919614 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919614/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919614 Building REAL300004919615 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919615' /scratch/stefan/7775247/working/building/REAL300004919615 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919615 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919615/0 /scratch/stefan/7775247/working/building/REAL300004919615 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/618 `/scratch/stefan/7775247/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)C=C(C)C([N+](=O)[O-])=C1C)C(=O)[O-]) `REAL300004919615.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919615 none CC#CCC(NC(=O)C1=C(C)C=C(C)C([N+](=O)[O-])=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 5, 1, 1, 5, 1, 8, 11, 11, 1, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 27, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 27, 40, 40, 61, 61, 61, 61, 61, 27, 6, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2] 61 rigid atoms, others: [33, 6, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39]) total number of confs: 309 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919615 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919615 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919615/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919615 Building REAL300004919616 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919616' /scratch/stefan/7775247/working/building/REAL300004919616 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919616 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919616/0 /scratch/stefan/7775247/working/building/REAL300004919616 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 619) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/619 `/scratch/stefan/7775247/working/3D/619' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC2CCCC2)N=C1)C(=O)[O-]) `REAL300004919616.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919616 none CC#CCC(NC(=O)C1=CC=C(OC2CCCC2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 9, 30, 30, 30, 30, 1, 1, 17, 27, 27, 47, 47, 47, 47, 47, 17, 5, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 18, 19, 41, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 287 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919616 none CC#CCC(NC(=O)C1=CC=C(OC2CCCC2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 124, 71, 71, 30, 71, 30, 30, 30, 6, 1, 1, 1, 1, 1, 1, 30, 30, 124, 154, 154, 201, 201, 201, 201, 201, 124, 71, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41]) total number of confs: 899 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919616 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919616 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919616/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919616 Building REAL300004919617 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919617' /scratch/stefan/7775247/working/building/REAL300004919617 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919617 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919617/0 /scratch/stefan/7775247/working/building/REAL300004919617 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/620 `/scratch/stefan/7775247/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN=C(OCC(C)C)C(Cl)=C1)C(=O)[O-]) `REAL300004919617.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919617 none CC#CCC(NC(=O)C1=CN=C(OCC(C)C)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 8, 1, 12, 5, 5, 5, 5, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 5, 20, 25, 34, 1, 1, 1, 15, 25, 25, 47, 47, 47, 47, 47, 15, 5, 1, 21, 21, 34, 34, 34, 34, 34, 34, 34, 1] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 17, 18, 19, 40, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 412 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919617 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919617 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919617/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919617 Building REAL300004919618 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919618' /scratch/stefan/7775247/working/building/REAL300004919618 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919618 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919618/0 /scratch/stefan/7775247/working/building/REAL300004919618 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 621) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/621 `/scratch/stefan/7775247/working/3D/621' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN=CN=C1C1=CC=CC=C1)C(=O)[O-]) `REAL300004919618.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919618 none CC#CCC(NC(=O)C1=CN=CN=C1C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [92, 92, 92, 36, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 36, 56, 56, 92, 92, 92, 92, 92, 36, 12, 1, 1, 4, 4, 2, 4, 4] 115 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 437 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919618 none CC#CCC(NC(=O)C1=CN=CN=C1C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [115, 115, 115, 55, 23, 23, 4, 23, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 55, 72, 72, 115, 115, 115, 115, 115, 55, 23, 4, 4, 1, 1, 1, 1, 1] 115 rigid atoms, others: [32, 33, 34, 35, 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]) total number of confs: 522 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919618 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919618 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919618/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919618 Building REAL300004919619 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919619' /scratch/stefan/7775247/working/building/REAL300004919619 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919619 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919619/0 /scratch/stefan/7775247/working/building/REAL300004919619 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/622 `/scratch/stefan/7775247/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CC(=O)N(C2=CC=C(Cl)C(F)=C2)C1)C(=O)[O-]) `REAL300004919619.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919619 none CC#CCC(NC(=O)C1CC(=O)N(C2=CC=C(Cl)C(F)=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 1, 1, 1, 1, 16, 1, 15, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 29, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 10, 10, 9, 9, 10, 10, 10, 1, 29, 46, 46, 67, 67, 67, 67, 67, 29, 10, 1, 1, 1, 10, 10, 10, 1, 1] 201 rigid atoms, others: [32, 33, 34, 38, 6, 39, 8, 9, 10, 11, 12, 13, 21] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 345 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: REAL300004919619 none CC#CCC(NC(=O)C1CC(=O)N(C2=CC=C(Cl)C(F)=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 1, 1, 1, 1, 16, 1, 15, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 111, 50, 50, 10, 50, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 111, 144, 144, 201, 201, 201, 201, 201, 111, 50, 10, 10, 10, 1, 1, 1, 10, 10] 201 rigid atoms, others: [35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39]) total number of confs: 927 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919619 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919619 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919619/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919619 Building REAL300004919620 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919620' /scratch/stefan/7775247/working/building/REAL300004919620 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919620 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919620/0 /scratch/stefan/7775247/working/building/REAL300004919620 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 623) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/623 `/scratch/stefan/7775247/working/3D/623' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN=CC(C2=CC=C3OCCC3=C2)=C1)C(=O)[O-]) `REAL300004919620.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919620 none CC#CCC(NC(=O)C1=CN=CC(C2=CC=C3OCCC3=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 21, 32, 32, 66, 66, 66, 66, 66, 21, 7, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1] 201 rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 12, 13, 22, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919620 none CC#CCC(NC(=O)C1=CN=CC(C2=CC=C3OCCC3=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 71, 21, 21, 5, 21, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 71, 104, 104, 201, 201, 201, 201, 201, 71, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42]) total number of confs: 931 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919620 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919620 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919620/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919620 Building REAL300004919621 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919621' /scratch/stefan/7775247/working/building/REAL300004919621 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919621 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919621/0 /scratch/stefan/7775247/working/building/REAL300004919621 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/624 `/scratch/stefan/7775247/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=C(S(=O)(=O)NCC)C=C1)C(=O)[O-]) `REAL300004919621.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919621 none CC#CCC(NC(=O)CC1=CC=C(S(=O)(=O)NCC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 27, 9, 9, 3, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 21, 1, 1, 27, 45, 45, 74, 74, 74, 74, 74, 27, 9, 3, 3, 1, 1, 7, 21, 21, 21, 21, 21, 1, 1] 201 rigid atoms, others: [33, 34, 8, 9, 10, 11, 12, 13, 19, 20, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 447 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919621 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919621 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919621/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919621 Building REAL300004919622 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919622' /scratch/stefan/7775247/working/building/REAL300004919622 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919622 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919622/0 /scratch/stefan/7775247/working/building/REAL300004919622 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 625) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/625 `/scratch/stefan/7775247/working/3D/625' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=CC(Cl)=C2)C(C)=C1)C(=O)[O-]) `REAL300004919622.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919622 none CC#CCC(NC(=O)C1=NN(C2=CC=CC(Cl)=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 25, 10, 9, 1, 9, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 1, 1, 1, 25, 36, 36, 63, 63, 63, 63, 63, 25, 10, 7, 7, 7, 7, 2, 2, 2, 1] 201 rigid atoms, others: [38, 6, 8, 9, 10, 11, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 313 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: REAL300004919622 none CC#CCC(NC(=O)C1=NN(C2=CC=CC(Cl)=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 85, 37, 37, 7, 37, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 85, 122, 122, 201, 201, 201, 201, 201, 85, 37, 1, 1, 1, 1, 7, 7, 7, 7] 201 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 943 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919622 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919622 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919622/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919622 Building REAL300004919623 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919623' /scratch/stefan/7775247/working/building/REAL300004919623 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919623 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919623/0 /scratch/stefan/7775247/working/building/REAL300004919623 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/626 `/scratch/stefan/7775247/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC(C)=CC(C)=C2)C(C)=C1)C(=O)[O-]) `REAL300004919623.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919623 none CC#CCC(NC(=O)C1=NN(C2=CC(C)=CC(C)=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 5, 1, 1, 5, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 35, 12, 13, 1, 13, 1, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 1, 1, 1, 35, 51, 51, 84, 84, 84, 84, 84, 35, 13, 6, 6, 6, 6, 1, 6, 6, 6, 6, 2, 2, 2, 1] 157 rigid atoms, others: [6, 8, 9, 10, 11, 44, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 411 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: REAL300004919623 none CC#CCC(NC(=O)C1=NN(C2=CC(C)=CC(C)=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 5, 1, 1, 5, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [159, 159, 159, 77, 37, 37, 6, 37, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 77, 105, 105, 159, 159, 159, 159, 159, 77, 37, 1, 2, 2, 2, 1, 2, 2, 2, 1, 6, 6, 6, 6] 159 rigid atoms, others: [32, 36, 40, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 37, 38, 39, 41, 42, 43, 44]) total number of confs: 749 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919623 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919623 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919623/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919623 Building REAL300004919624 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919624' /scratch/stefan/7775247/working/building/REAL300004919624 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919624 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919624/0 /scratch/stefan/7775247/working/building/REAL300004919624 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 627) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/627 `/scratch/stefan/7775247/working/3D/627' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CSC1=CC=C(Cl)C=C1[N+](=O)[O-])C(=O)[O-]) `REAL300004919624.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919624 none CC#CCC(NC(=O)CSC1=CC=C(Cl)C=C1[N+](=O)[O-])C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 14, 1, 1, 1, 1, 16, 1, 1, 8, 11, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 109, 64, 64, 16, 64, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 109, 153, 153, 201, 201, 201, 201, 201, 109, 64, 16, 16, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 1003 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919624 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919624 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919624/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919624 Building REAL300004919625 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919625' /scratch/stefan/7775247/working/building/REAL300004919625 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919625 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919625/0 /scratch/stefan/7775247/working/building/REAL300004919625 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/628 `/scratch/stefan/7775247/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(C)N=C1C1=CC=CS1)C(=O)[O-]) `REAL300004919625.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919625 none CC#CCC(NC(=O)C1=CN(C)N=C1C1=CC=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 42, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 42, 63, 63, 107, 107, 107, 107, 107, 42, 12, 1, 2, 2, 2, 12, 12, 12] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 29] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 523 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919625 none CC#CCC(NC(=O)C1=CN(C)N=C1C1=CC=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 110, 58, 58, 12, 58, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 110, 149, 149, 201, 201, 201, 201, 201, 110, 58, 12, 12, 12, 12, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 943 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919625 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919625 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919625/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919625 Building REAL300004919626 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919626' /scratch/stefan/7775247/working/building/REAL300004919626 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919626 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919626/0 /scratch/stefan/7775247/working/building/REAL300004919626 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 629) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/629 `/scratch/stefan/7775247/working/3D/629' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C2C(=C1)CCC(=O)N2C)C(=O)[O-]) `REAL300004919626.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919626 none CC#CCC(NC(=O)C1=CC=C2C(=C1)CCC(=O)N2C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 31, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 42, 42, 70, 70, 70, 70, 70, 31, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 70 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 38, 7, 39, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37]) total number of confs: 326 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919626 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919626 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919626/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919626 Building REAL300004919627 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919627' /scratch/stefan/7775247/working/building/REAL300004919627 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919627 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919627/0 /scratch/stefan/7775247/working/building/REAL300004919627 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/630 `/scratch/stefan/7775247/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN=C(CC2=CC=CC=C2)S1)C(=O)[O-]) `REAL300004919627.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919627 none CC#CCC(NC(=O)C1=CN=C(CC2=CC=CC=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 21, 8, 8, 1, 8, 1, 1, 1, 1, 1, 8, 16, 16, 12, 16, 16, 1, 21, 36, 36, 63, 63, 63, 63, 63, 21, 8, 1, 8, 8, 16, 16, 12, 16, 16] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919627 none CC#CCC(NC(=O)C1=CN=C(CC2=CC=CC=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 115, 62, 62, 16, 62, 16, 16, 16, 4, 1, 1, 1, 1, 1, 1, 1, 16, 115, 145, 145, 201, 201, 201, 201, 201, 115, 62, 16, 4, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 931 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919627 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919627 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919627/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919627 Building REAL300004919628 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919628' /scratch/stefan/7775247/working/building/REAL300004919628 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919628 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919628/0 /scratch/stefan/7775247/working/building/REAL300004919628 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 631) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/631 `/scratch/stefan/7775247/working/3D/631' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Cl)=CC=C1SC1=CC=CC=C1)C(=O)[O-]) `REAL300004919628.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919628 none CC#CCC(NC(=O)C1=CC(Cl)=CC=C1SC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 29, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 9, 23, 20, 12, 23, 23, 29, 42, 42, 69, 69, 69, 69, 69, 29, 11, 1, 1, 1, 23, 23, 12, 23, 23] 201 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39]) total number of confs: 382 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919628 none CC#CCC(NC(=O)C1=CC(Cl)=CC=C1SC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 1, 1, 14, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 123, 73, 77, 23, 77, 23, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 1, 1, 1, 123, 152, 152, 201, 201, 201, 201, 201, 123, 77, 23, 23, 23, 1, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 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]) total number of confs: 905 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919628 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919628 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919628/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919628 Building REAL300004919629 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919629' /scratch/stefan/7775247/working/building/REAL300004919629 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919629 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919629/0 /scratch/stefan/7775247/working/building/REAL300004919629 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/632 `/scratch/stefan/7775247/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)[C@@H]1CCCN1C(=O)NC(C)C)C(=O)[O-]) `REAL300004919629.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919629 none CC#CCC(NC(=O)[C@@H]1CCCN1C(=O)NC(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 8, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 2, 2, 7, 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: [104, 104, 104, 35, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 35, 59, 59, 104, 104, 104, 104, 104, 35, 10, 1, 1, 1, 1, 1, 1, 5, 19, 19, 19, 19, 19, 19, 19] 189 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 571 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919629 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919629 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919629/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919629 Building REAL300004919630 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919630' /scratch/stefan/7775247/working/building/REAL300004919630 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919630 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919630/0 /scratch/stefan/7775247/working/building/REAL300004919630 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 633) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/633 `/scratch/stefan/7775247/working/3D/633' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)CC)=C1)C(=O)[O-]) `REAL300004919630.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919630 none CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)CC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 5, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 11, 1, 17, 26, 26, 60, 60, 60, 60, 60, 17, 5, 1, 1, 1, 11, 11, 11, 11, 11, 1] 201 rigid atoms, others: [37, 6, 8, 9, 10, 11, 12, 13, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36]) total number of confs: 302 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919630 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919630 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919630/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919630 Building REAL300004919631 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919631' /scratch/stefan/7775247/working/building/REAL300004919631 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919631 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919631/0 /scratch/stefan/7775247/working/building/REAL300004919631 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/634 `/scratch/stefan/7775247/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CNC2=CC=CC(OC)=C12)C(=O)[O-]) `REAL300004919631.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919631 none CC#CCC(NC(=O)CC1=CNC2=CC=CC(OC)=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 1, 1, 8, 1, 1, 1, 1, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [167, 167, 167, 77, 39, 39, 6, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 77, 115, 115, 167, 167, 167, 167, 167, 77, 39, 6, 6, 1, 1, 1, 1, 1, 4, 4, 4] 201 rigid atoms, others: [32, 33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39]) total number of confs: 838 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919631 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919631 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919631/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919631 Building REAL300004919632 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919632' /scratch/stefan/7775247/working/building/REAL300004919632 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919632 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919632/0 /scratch/stefan/7775247/working/building/REAL300004919632 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 635) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/635 `/scratch/stefan/7775247/working/3D/635' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2Cl)C(C)=C1)C(=O)[O-]) `REAL300004919632.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919632 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2Cl)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [115, 115, 115, 41, 11, 11, 1, 11, 1, 1, 1, 1, 7, 7, 2, 7, 7, 7, 1, 1, 1, 41, 64, 64, 115, 115, 115, 115, 115, 41, 11, 7, 7, 2, 7, 2, 2, 2, 1] 180 rigid atoms, others: [38, 6, 8, 9, 10, 11, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 557 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919632 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2Cl)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [180, 180, 180, 98, 43, 43, 7, 43, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 98, 127, 127, 180, 180, 180, 180, 180, 98, 43, 1, 1, 1, 1, 7, 7, 7, 7] 180 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 820 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919632 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919632 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919632/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919632 Building REAL300004919633 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919633' /scratch/stefan/7775247/working/building/REAL300004919633 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919633 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919633/0 /scratch/stefan/7775247/working/building/REAL300004919633 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/636 `/scratch/stefan/7775247/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1COC2=CC=C(Br)C=C21)C(=O)[O-]) `REAL300004919633.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919633 none CC#CCC(NC(=O)C1COC2=CC=C(Br)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 43, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 58, 58, 95, 95, 95, 95, 95, 43, 13, 1, 1, 1, 1, 1, 1] 95 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 432 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919633 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919633 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919633/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919633 Building REAL300004919634 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919634' /scratch/stefan/7775247/working/building/REAL300004919634 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919634 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919634/0 /scratch/stefan/7775247/working/building/REAL300004919634 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 637) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/637 `/scratch/stefan/7775247/working/3D/637' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC(F)=CC=C1Br)C(=O)[O-]) `REAL300004919634.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919634 none CC#CCC(NC(=O)CCC1=CC(F)=CC=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 15, 1, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 106, 49, 49, 10, 49, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 106, 139, 139, 201, 201, 201, 201, 201, 106, 49, 10, 10, 6, 6, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 964 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919634 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919634 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919634/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919634 Building REAL300004919635 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919635' /scratch/stefan/7775247/working/building/REAL300004919635 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919635 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919635/0 /scratch/stefan/7775247/working/building/REAL300004919635 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/638 `/scratch/stefan/7775247/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=C(F)C=C2F)CCC1)C(=O)[O-]) `REAL300004919635.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919635 none CC#CCC(NC(=O)C1(C2=CC=C(F)C=C2F)CCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 1, 1, 1, 1, 15, 1, 1, 15, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 120, 120, 45, 11, 11, 1, 11, 1, 1, 7, 7, 1, 6, 7, 7, 7, 1, 1, 1, 45, 70, 70, 120, 120, 120, 120, 120, 45, 11, 7, 7, 7, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 17, 18, 19, 38] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 594 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919635 none CC#CCC(NC(=O)C1(C2=CC=C(F)C=C2F)CCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 1, 1, 1, 1, 15, 1, 1, 15, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 95, 35, 35, 7, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 95, 132, 132, 201, 201, 201, 201, 201, 95, 35, 1, 1, 1, 7, 7, 7, 7, 7, 7] 201 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 952 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919635 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919635 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919635/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919635 Building REAL300004919636 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919636' /scratch/stefan/7775247/working/building/REAL300004919636 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919636 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919636/0 /scratch/stefan/7775247/working/building/REAL300004919636 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 639) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/639 `/scratch/stefan/7775247/working/3D/639' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=C(F)C=C2F)CCCC1)C(=O)[O-]) `REAL300004919636.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919636 none CC#CCC(NC(=O)C1(C2=CC=C(F)C=C2F)CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 15, 1, 1, 15, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 32, 12, 12, 1, 12, 1, 1, 8, 8, 1, 7, 8, 8, 8, 1, 1, 1, 1, 32, 50, 50, 93, 93, 93, 93, 93, 32, 12, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1] 155 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 17, 18, 19, 20, 41, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 460 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: REAL300004919636 none CC#CCC(NC(=O)C1(C2=CC=C(F)C=C2F)CCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 15, 1, 1, 15, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [155, 155, 155, 66, 28, 28, 8, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 66, 97, 97, 155, 155, 155, 155, 155, 66, 28, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8] 155 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 745 number of broken/clashed sets: 82 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919636 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919636 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919636/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919636 Building REAL300004919637 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919637' /scratch/stefan/7775247/working/building/REAL300004919637 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919637 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919637/0 /scratch/stefan/7775247/working/building/REAL300004919637 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/640 `/scratch/stefan/7775247/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC=C(S(=O)(=O)CC)C=C1)C(=O)[O-]) `REAL300004919637.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919637 none CC#CCC(NC(=O)CCC1=CC=C(S(=O)(=O)CC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 1, 1, 1, 1, 14, 11, 11, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 6, 3, 3, 2, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 1, 1, 6, 8, 8, 17, 17, 17, 17, 17, 6, 3, 2, 2, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1] 23 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 43, 19, 20, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919637 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919637 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919637/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919637 Building REAL300004919638 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919638' /scratch/stefan/7775247/working/building/REAL300004919638 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919638 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919638/0 /scratch/stefan/7775247/working/building/REAL300004919638 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 641) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/641 `/scratch/stefan/7775247/working/3D/641' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NC2=CC(Cl)=CC=C2C=C1)C(=O)[O-]) `REAL300004919638.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919638 none CC#CCC(NC(=O)C1=NC2=CC(Cl)=CC=C2C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 28, 11, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 39, 39, 57, 57, 57, 57, 57, 28, 12, 1, 1, 1, 1, 1] 57 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 277 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919638 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919638 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919638/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919638 Building REAL300004919639 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919639' /scratch/stefan/7775247/working/building/REAL300004919639 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919639 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919639/0 /scratch/stefan/7775247/working/building/REAL300004919639 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/642 `/scratch/stefan/7775247/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(Br)N=CS1)C(=O)[O-]) `REAL300004919639.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919639 none CC#CCC(NC(=O)C1=C(Br)N=CS1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Br', 'N.2', 'C.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 17, 8, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 24, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 24, 37, 37, 48, 48, 48, 48, 48, 24, 5, 1] 65 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 24] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919639 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919639 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919639/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919639 Building REAL300004919640 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919640' /scratch/stefan/7775247/working/building/REAL300004919640 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919640 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919640/0 /scratch/stefan/7775247/working/building/REAL300004919640 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 643) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/643 `/scratch/stefan/7775247/working/3D/643' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(OC1=CC=CC(Cl)=C1)C(C)C)C(=O)[O-]) `REAL300004919640.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919640 none CC#CCC(NC(=O)C(OC1=CC=CC(Cl)=C1)C(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 16, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [166, 166, 166, 94, 57, 57, 13, 57, 8, 1, 1, 1, 1, 1, 1, 1, 1, 13, 38, 38, 94, 130, 130, 166, 166, 166, 166, 166, 94, 57, 13, 1, 1, 1, 1, 38, 38, 38, 38, 38, 38, 38] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 965 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919640 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919640 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919640/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919640 Building REAL300004919641 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919641' /scratch/stefan/7775247/working/building/REAL300004919641 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919641 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919641/0 /scratch/stefan/7775247/working/building/REAL300004919641 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/644 `/scratch/stefan/7775247/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=NC(OCCOC)=C1)C(=O)[O-]) `REAL300004919641.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919641 none CC#CCC(NC(=O)C1=CC=NC(OCCOC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 8, 1, 12, 5, 5, 12, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 3, 14, 19, 37, 1, 14, 22, 22, 39, 39, 39, 39, 39, 14, 5, 1, 1, 14, 14, 19, 19, 37, 37, 37, 1] 201 rigid atoms, others: [38, 6, 8, 9, 10, 11, 12, 13, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919641 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919641 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919641/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919641 Building REAL300004919642 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919642' /scratch/stefan/7775247/working/building/REAL300004919642 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919642 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919642/0 /scratch/stefan/7775247/working/building/REAL300004919642 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 645) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/645 `/scratch/stefan/7775247/working/3D/645' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC([N+](=O)[O-])=CC=C1SCC)C(=O)[O-]) `REAL300004919642.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919642 none CC#CCC(NC(=O)C1=CC([N+](=O)[O-])=CC=C1SCC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 8, 11, 11, 1, 1, 1, 14, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 31, 11, 11, 1, 11, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 32, 31, 52, 52, 86, 86, 86, 86, 86, 31, 11, 1, 1, 1, 32, 32, 33, 33, 33] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37]) total number of confs: 531 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919642 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919642 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919642/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919642 Building REAL300004919643 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919643' /scratch/stefan/7775247/working/building/REAL300004919643 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919643 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919643/0 /scratch/stefan/7775247/working/building/REAL300004919643 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/646 `/scratch/stefan/7775247/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN=C(OCC2CC2)C(Cl)=C1)C(=O)[O-]) `REAL300004919643.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919643 none CC#CCC(NC(=O)C1=CN=C(OCC2CC2)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 8, 1, 12, 5, 5, 5, 5, 1, 16, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 5, 20, 42, 42, 1, 1, 1, 15, 23, 23, 41, 41, 41, 41, 41, 15, 5, 1, 20, 20, 42, 42, 42, 42, 42, 1] 201 rigid atoms, others: [38, 6, 8, 9, 10, 11, 12, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 317 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919643 none CC#CCC(NC(=O)C1=CN=C(OCC2CC2)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 8, 1, 12, 5, 5, 5, 5, 1, 16, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 87, 87, 42, 87, 42, 42, 42, 28, 8, 1, 1, 1, 1, 42, 42, 42, 131, 159, 159, 201, 201, 201, 201, 201, 131, 87, 42, 8, 8, 1, 1, 1, 1, 1, 42] 201 rigid atoms, others: [33, 34, 35, 36, 37, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38]) total number of confs: 881 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919643 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919643 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919643/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919643 Building REAL300004919644 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919644' /scratch/stefan/7775247/working/building/REAL300004919644 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919644 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919644/0 /scratch/stefan/7775247/working/building/REAL300004919644 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 647) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/647 `/scratch/stefan/7775247/working/3D/647' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CN(C)S(=O)(=O)C1=CC=CN=C1)C(=O)[O-]) `REAL300004919644.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919644 none CC#CCC(NC(=O)CN(C)S(=O)(=O)C1=CC=CN=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 8, 5, 14, 11, 11, 1, 1, 1, 1, 8, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 83, 48, 48, 24, 48, 17, 8, 17, 1, 8, 8, 1, 1, 1, 1, 1, 1, 83, 86, 86, 99, 99, 99, 99, 99, 83, 48, 24, 24, 18, 18, 18, 1, 1, 1, 1] 99 rigid atoms, others: [35, 36, 37, 38, 11, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 464 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919644 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919644 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919644/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919644 Building REAL300004919645 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919645' /scratch/stefan/7775247/working/building/REAL300004919645 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919645 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919645/0 /scratch/stefan/7775247/working/building/REAL300004919645 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/648 `/scratch/stefan/7775247/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCN(S(=O)(=O)C2=CC=CN=C2)CC1)C(=O)[O-]) `REAL300004919645.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919645 none CC#CCC(NC(=O)C1CCN(S(=O)(=O)C2=CC=CN=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 28, 12, 12, 1, 12, 1, 1, 1, 1, 1, 6, 6, 6, 21, 21, 20, 21, 21, 1, 1, 28, 43, 43, 62, 62, 62, 62, 62, 28, 12, 1, 1, 1, 1, 1, 21, 21, 20, 21, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 45, 44, 43, 21, 22, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41]) total number of confs: 337 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919645 none CC#CCC(NC(=O)C1CCN(S(=O)(=O)C2=CC=CN=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 8, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 128, 79, 79, 21, 79, 21, 21, 21, 7, 1, 7, 7, 1, 1, 1, 1, 1, 1, 21, 21, 128, 161, 161, 201, 201, 201, 201, 201, 128, 79, 21, 21, 21, 21, 21, 1, 1, 1, 1, 21, 21, 21, 21] 201 rigid atoms, others: [38, 39, 40, 41, 12, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45]) total number of confs: 931 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919645 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919645 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919645/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919645 Building REAL300004919646 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919646' /scratch/stefan/7775247/working/building/REAL300004919646 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919646 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919646/0 /scratch/stefan/7775247/working/building/REAL300004919646 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 649) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/649 `/scratch/stefan/7775247/working/3D/649' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(OCC2=CC=CC=N2)C=C1)C(=O)[O-]) `REAL300004919646.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919646 none CC#CCC(NC(=O)C=CC1=CC=C(OCC2=CC=CC=N2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 36, 17, 17, 3, 17, 3, 1, 1, 1, 1, 1, 1, 2, 2, 14, 14, 14, 14, 14, 1, 1, 36, 54, 54, 66, 66, 66, 66, 66, 36, 17, 3, 3, 1, 1, 2, 2, 14, 14, 14, 14, 1, 1] 201 rigid atoms, others: [45, 36, 37, 9, 10, 11, 12, 13, 14, 44, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43]) total number of confs: 346 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: REAL300004919646 none CC#CCC(NC(=O)C=CC1=CC=C(OCC2=CC=CC=N2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 90, 90, 27, 90, 27, 14, 14, 14, 14, 7, 7, 1, 1, 1, 1, 1, 1, 1, 14, 14, 139, 159, 159, 201, 201, 201, 201, 201, 139, 90, 27, 27, 14, 14, 7, 7, 1, 1, 1, 1, 14, 14] 201 rigid atoms, others: [40, 41, 42, 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, 44, 45]) total number of confs: 905 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919646 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919646 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919646/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919646 Building REAL300004919647 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919647' /scratch/stefan/7775247/working/building/REAL300004919647 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919647 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919647/0 /scratch/stefan/7775247/working/building/REAL300004919647 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/650 `/scratch/stefan/7775247/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(F)=CC=C1[N-]S(C)(=O)=O)C(=O)[O-]) `REAL300004919647.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919647 none CC#CCC(NC(=O)C1=CC(F)=CC=C1[N-]S(C)(=O)=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 15, 1, 1, 1, 8, 14, 5, 11, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 2, 2, 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: [7, 7, 7, 4, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 4, 4, 4, 7, 7, 7, 7, 7, 4, 3, 1, 1, 1, 3, 3, 3] 9 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919647 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919647 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919647/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919647 Building REAL300004919648 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919648' /scratch/stefan/7775247/working/building/REAL300004919648 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919648 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919648/0 /scratch/stefan/7775247/working/building/REAL300004919648 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 651) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/651 `/scratch/stefan/7775247/working/3D/651' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CN1C(=O)C2=CC=CC=C2N2C(=O)CCC21C)C(=O)[O-]) `REAL300004919648.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919648 none CC#CCC(NC(=O)CN1C(=O)C2=CC=CC=C2N2C(=O)CCC21C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 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: [132, 132, 132, 79, 27, 27, 6, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 79, 104, 104, 132, 132, 132, 132, 132, 79, 27, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 132 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 37, 38, 39, 40, 41, 42, 43, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46, 47]) total number of confs: 663 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919648 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919648 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919648/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919648 Building REAL300004919649 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919649' /scratch/stefan/7775247/working/building/REAL300004919649 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919649 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919649/0 /scratch/stefan/7775247/working/building/REAL300004919649 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/652 `/scratch/stefan/7775247/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C2CC2)=NC2=C1C(=O)NC(=O)N2CC)C(=O)[O-]) `REAL300004919649.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919649 none CC#CCC(NC(=O)C1=CC(C2CC2)=NC2=C1C(=O)NC(=O)N2CC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 1, 1, 1, 11, 8, 1, 11, 8, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 22, 7, 7, 1, 7, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 22, 37, 37, 68, 68, 68, 68, 68, 22, 7, 1, 11, 11, 11, 11, 11, 1, 2, 2, 3, 3, 3] 201 rigid atoms, others: [35, 6, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 41, 23] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 361 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919649 none CC#CCC(NC(=O)C1=CC(C2CC2)=NC2=C1C(=O)NC(=O)N2CC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 1, 1, 1, 11, 8, 1, 11, 8, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 104, 72, 42, 42, 11, 42, 11, 11, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 21, 72, 85, 85, 104, 104, 104, 104, 104, 72, 42, 11, 1, 1, 1, 1, 1, 11, 21, 21, 21, 21, 21] 201 rigid atoms, others: [36, 37, 38, 39, 40, 10, 11, 12, 13] 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, 41, 42, 43, 44, 45, 46]) total number of confs: 519 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919649 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919649 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919649/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919649 Building REAL300004919650 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919650' /scratch/stefan/7775247/working/building/REAL300004919650 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919650 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919650/0 /scratch/stefan/7775247/working/building/REAL300004919650 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 653) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/653 `/scratch/stefan/7775247/working/3D/653' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C(C)C)=NC2=C1C(=O)NC(=O)N2CC)C(=O)[O-]) `REAL300004919650.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919650 none CC#CCC(NC(=O)C1=CC(C(C)C)=NC2=C1C(=O)NC(=O)N2CC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 1, 1, 1, 11, 8, 1, 11, 8, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 2, 2, 7, 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: [48, 48, 48, 18, 7, 7, 1, 7, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 30, 30, 48, 48, 48, 48, 48, 18, 7, 1, 5, 5, 5, 5, 5, 5, 5, 1, 2, 2, 2, 2, 2] 144 rigid atoms, others: [35, 6, 8, 9, 10, 11, 43, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 264 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919650 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919650 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919650/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919650 Building REAL300004919651 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919651' /scratch/stefan/7775247/working/building/REAL300004919651 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919651 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919651/0 /scratch/stefan/7775247/working/building/REAL300004919651 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/654 `/scratch/stefan/7775247/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(CC)N(CC2=CC=CC=C2)N=C1)C(=O)[O-]) `REAL300004919651.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919651 none CC#CCC(NC(=O)C1=C(CC)N(CC2=CC=CC=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 20, 10, 10, 1, 10, 1, 1, 1, 2, 1, 1, 5, 9, 9, 7, 9, 9, 1, 1, 20, 30, 30, 44, 44, 44, 44, 44, 20, 10, 2, 2, 3, 3, 3, 5, 5, 9, 9, 9, 9, 9, 1] 201 rigid atoms, others: [6, 8, 9, 10, 12, 13, 44, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 11, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 259 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: REAL300004919651 none CC#CCC(NC(=O)C1=C(CC)N(CC2=CC=CC=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [135, 135, 135, 74, 42, 42, 9, 42, 9, 9, 9, 16, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 74, 104, 104, 135, 135, 135, 135, 135, 74, 42, 16, 16, 17, 17, 17, 3, 3, 1, 1, 1, 1, 1, 9] 201 rigid atoms, others: [39, 40, 41, 42, 43, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44]) total number of confs: 718 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919651 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919651 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919651/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919651 Building REAL300004919652 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919652' /scratch/stefan/7775247/working/building/REAL300004919652 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919652 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919652/0 /scratch/stefan/7775247/working/building/REAL300004919652 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 655) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/655 `/scratch/stefan/7775247/working/3D/655' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CSC(C2=CC=C(Cl)C(Cl)=C2)=N1)C(=O)[O-]) `REAL300004919652.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919652 none CC#CCC(NC(=O)C1=CSC(C2=CC=C(Cl)C(Cl)=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 16, 1, 16, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [98, 98, 98, 36, 12, 11, 1, 11, 1, 1, 1, 1, 1, 5, 5, 2, 2, 5, 5, 5, 1, 36, 55, 55, 98, 98, 98, 98, 98, 36, 12, 1, 5, 5, 5] 145 rigid atoms, others: [6, 8, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34]) total number of confs: 476 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919652 none CC#CCC(NC(=O)C1=CSC(C2=CC=C(Cl)C(Cl)=C2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 16, 1, 16, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [145, 145, 145, 84, 36, 36, 5, 36, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 84, 110, 110, 145, 145, 145, 145, 145, 84, 36, 5, 1, 1, 1] 145 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 687 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919652 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919652 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919652/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919652 Building REAL300004919653 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919653' /scratch/stefan/7775247/working/building/REAL300004919653 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919653 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919653/0 /scratch/stefan/7775247/working/building/REAL300004919653 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/656 `/scratch/stefan/7775247/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCC1=NC(C2=CC=C(F)C=C2)=NO1)C(=O)[O-]) `REAL300004919653.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919653 none CC#CCC(NC(=O)CCCC1=NC(C2=CC=C(F)C=C2)=NO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 8, 12, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 183, 178, 178, 40, 178, 17, 9, 1, 1, 1, 1, 1, 4, 4, 1, 1, 4, 4, 1, 1, 183, 188, 188, 200, 200, 200, 200, 200, 183, 178, 40, 40, 17, 17, 9, 9, 4, 4, 4, 4] 201 rigid atoms, others: [10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 690 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919653 none CC#CCC(NC(=O)CCCC1=NC(C2=CC=C(F)C=C2)=NO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'O.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 8, 12, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 184, 180, 180, 47, 180, 24, 15, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 184, 188, 188, 201, 201, 201, 201, 201, 184, 180, 47, 47, 24, 24, 15, 15, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 686 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919653 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919653 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919653/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919653 Building REAL300004919654 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919654' /scratch/stefan/7775247/working/building/REAL300004919654 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004919654 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919654/0 /scratch/stefan/7775247/working/building/REAL300004919654 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 657) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/657 `/scratch/stefan/7775247/working/3D/657' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=C(C)N=C(C2=CC=CN=C2)NC1=O)C(=O)[O-]) `REAL300004919654.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919654 none CC#CCC(NC(=O)CC1=C(C)N=C(C2=CC=CN=C2)NC1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 1, 1, 5, 8, 1, 1, 1, 1, 1, 8, 1, 8, 1, 11, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 36, 17, 17, 3, 17, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 1, 1, 1, 36, 59, 59, 86, 86, 86, 86, 86, 36, 17, 3, 3, 1, 1, 1, 11, 11, 11, 11, 1] 201 rigid atoms, others: [35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41]) total number of confs: 448 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919654 none CC#CCC(NC(=O)CC1=C(C)N=C(C2=CC=CN=C2)NC1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 1, 1, 5, 8, 1, 1, 1, 1, 1, 8, 1, 8, 1, 11, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 127, 77, 77, 19, 77, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 127, 164, 164, 201, 201, 201, 201, 201, 127, 77, 19, 19, 11, 11, 11, 1, 1, 1, 1, 11] 201 rigid atoms, others: [38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42]) total number of confs: 986 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919654 /scratch/stefan/7775247/working /scratch/stefan/7775247 mkdir: created directory `1' /scratch/stefan/7775247/working/building/REAL300004919654/1 /scratch/stefan/7775247/working/building/REAL300004919654 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 1 (index: 658) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/658 `/scratch/stefan/7775247/working/3D/658' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=C(C)N=C(C2=CC=CN=C2)[N-]C1=O)C(=O)[O-]) `REAL300004919654.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004919654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919654/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919654 none CC#CCC(NC(=O)CC1=C(C)N=C(C2=CC=CN=C2)[N-]C1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 1, 1, 5, 8, 1, 1, 1, 1, 1, 8, 1, 8, 1, 11, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 42, 20, 20, 4, 20, 1, 1, 1, 1, 1, 1, 1, 12, 12, 11, 12, 12, 1, 1, 1, 42, 60, 60, 96, 96, 96, 96, 96, 42, 20, 4, 4, 1, 1, 1, 12, 12, 11, 12] 201 rigid atoms, others: [35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41]) total number of confs: 466 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: REAL300004919654 none CC#CCC(NC(=O)CC1=C(C)N=C(C2=CC=CN=C2)[N-]C1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 1, 1, 5, 8, 1, 1, 1, 1, 1, 8, 1, 8, 1, 11, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 82, 82, 22, 82, 11, 11, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 138, 169, 169, 201, 201, 201, 201, 201, 138, 82, 22, 22, 12, 12, 12, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 939 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919654 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919654 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 1: /scratch/stefan/7775247/working/building/REAL300004919654/1.* 0: /scratch/stefan/7775247/working/building/REAL300004919654/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919654 Building REAL300004919655 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919655' /scratch/stefan/7775247/working/building/REAL300004919655 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919655 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919655/0 /scratch/stefan/7775247/working/building/REAL300004919655 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 659) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/659 `/scratch/stefan/7775247/working/3D/659' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=C(C=C1F)NC(=O)CC2)C(=O)[O-]) `REAL300004919655.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919655 none CC#CCC(NC(=O)C1=CC2=C(C=C1F)NC(=O)CC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 8, 1, 11, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 40, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 54, 54, 79, 79, 79, 79, 79, 40, 12, 1, 1, 1, 1, 1, 1, 1] 79 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 378 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919655 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919655 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919655/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919655 Building REAL300004919656 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919656' /scratch/stefan/7775247/working/building/REAL300004919656 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919656 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919656/0 /scratch/stefan/7775247/working/building/REAL300004919656 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/660 `/scratch/stefan/7775247/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C2C(C)=NN(C(C)(C)C)C2=NC(C2CC2)=C1)C(=O)[O-]) `REAL300004919656.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919656 none CC#CCC(NC(=O)C1=C2C(C)=NN(C(C)(C)C)C2=NC(C2CC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 5, 8, 8, 5, 5, 5, 5, 1, 8, 1, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 30, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 11, 11, 1, 30, 49, 49, 92, 92, 92, 92, 92, 30, 9, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 1] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 24, 52] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 22, 23, 25, 26, 27, 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: 477 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919656 none CC#CCC(NC(=O)C1=C2C(C)=NN(C(C)(C)C)C2=NC(C2CC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 5, 8, 8, 5, 5, 5, 5, 1, 8, 1, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 181, 181, 110, 55, 55, 11, 55, 11, 11, 11, 11, 11, 11, 11, 23, 23, 23, 11, 11, 1, 1, 1, 1, 11, 110, 138, 138, 181, 181, 181, 181, 181, 110, 55, 11, 11, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 11] 201 rigid atoms, others: [47, 48, 49, 50, 51, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 52]) total number of confs: 881 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919656 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919656 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919656/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919656 Building REAL300004919657 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919657' /scratch/stefan/7775247/working/building/REAL300004919657 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919657 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919657/0 /scratch/stefan/7775247/working/building/REAL300004919657 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 661) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/661 `/scratch/stefan/7775247/working/3D/661' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C2C(C)=NN(C(C)(C)C)C2=NC(C(C)C)=C1)C(=O)[O-]) `REAL300004919657.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919657 none CC#CCC(NC(=O)C1=C2C(C)=NN(C(C)(C)C)C2=NC(C(C)C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 5, 8, 8, 5, 5, 5, 5, 1, 8, 1, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 29, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 5, 5, 1, 29, 48, 48, 85, 85, 85, 85, 85, 29, 9, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 1] 171 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 54, 24] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 22, 23, 25, 26, 27, 28, 29, 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: 443 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919657 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919657 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919657/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919657 Building REAL300004919658 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919658' /scratch/stefan/7775247/working/building/REAL300004919658 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919658 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919658/0 /scratch/stefan/7775247/working/building/REAL300004919658 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/662 `/scratch/stefan/7775247/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Cl)=CC2=CC=CN=C21)C(=O)[O-]) `REAL300004919658.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919658 none CC#CCC(NC(=O)C1=CC(Cl)=CC2=CC=CN=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 31, 12, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 48, 48, 78, 78, 78, 78, 78, 31, 13, 1, 1, 1, 1, 1] 78 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 390 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919658 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919658 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919658/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919658 Building REAL300004919659 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919659' /scratch/stefan/7775247/working/building/REAL300004919659 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919659 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919659/0 /scratch/stefan/7775247/working/building/REAL300004919659 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 663) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/663 `/scratch/stefan/7775247/working/3D/663' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1[N-]S(=O)(=O)CCC)C(=O)[O-]) `REAL300004919659.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919659 none CC#CCC(NC(=O)C1=CC=CC=C1[N-]S(=O)(=O)CCC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 11, 11, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 4, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 4, 4, 4, 7, 7, 7, 7, 7, 4, 3, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3] 8 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919659 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919659 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919659/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919659 Building REAL300004919660 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919660' /scratch/stefan/7775247/working/building/REAL300004919660 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919660 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919660/0 /scratch/stefan/7775247/working/building/REAL300004919660 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/664 `/scratch/stefan/7775247/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)[C@H](C)NC(=O)C1CCCCC1)C(=O)[O-]) `REAL300004919660.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919660 none CC#CCC(NC(=O)[C@H](C)NC(=O)C1CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 78, 78, 24, 78, 9, 24, 24, 9, 1, 9, 1, 1, 1, 1, 1, 1, 131, 174, 174, 201, 201, 201, 201, 201, 131, 78, 24, 24, 24, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 1029 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919660 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919660 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919660/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919660 Building REAL300004919661 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919661' /scratch/stefan/7775247/working/building/REAL300004919661 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919661 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919661/0 /scratch/stefan/7775247/working/building/REAL300004919661 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 665) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/665 `/scratch/stefan/7775247/working/3D/665' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC(C)C1=CC=C(F)C=C1F)C(=O)[O-]) `REAL300004919661.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919661 none CC#CCC(NC(=O)CC(C)C1=CC=C(F)C=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 15, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 108, 58, 58, 14, 58, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 108, 142, 142, 201, 201, 201, 201, 201, 108, 58, 14, 14, 6, 6, 6, 6, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 9, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 975 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919661 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919661 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919661/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919661 Building REAL300004919662 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919662' /scratch/stefan/7775247/working/building/REAL300004919662 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919662 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919662/0 /scratch/stefan/7775247/working/building/REAL300004919662 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/666 `/scratch/stefan/7775247/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C2CC2)N(CC(C)C)N=C1)C(=O)[O-]) `REAL300004919662.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919662 none CC#CCC(NC(=O)C1=C(C2CC2)N(CC(C)C)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 5, 5, 8, 5, 5, 5, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 113, 43, 13, 13, 1, 13, 1, 1, 1, 5, 5, 1, 1, 4, 7, 7, 1, 1, 43, 68, 68, 113, 113, 113, 113, 113, 43, 13, 5, 5, 5, 5, 5, 4, 4, 7, 7, 7, 7, 7, 7, 7, 1] 201 rigid atoms, others: [6, 8, 9, 10, 44, 13, 14, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 569 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: REAL300004919662 none CC#CCC(NC(=O)C1=C(C2CC2)N(CC(C)C)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 5, 5, 8, 5, 5, 5, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [132, 132, 132, 61, 22, 22, 5, 22, 5, 1, 1, 1, 1, 5, 5, 11, 13, 13, 5, 5, 61, 88, 88, 132, 132, 132, 132, 132, 61, 22, 1, 1, 1, 1, 1, 11, 11, 13, 13, 13, 13, 13, 13, 13, 5] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 30, 31] 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 671 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919662 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919662 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919662/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919662 Building REAL300004919663 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919663' /scratch/stefan/7775247/working/building/REAL300004919663 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919663 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919663/0 /scratch/stefan/7775247/working/building/REAL300004919663 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 667) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/667 `/scratch/stefan/7775247/working/3D/667' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(CC)N(CC(C)C)N=C1)C(=O)[O-]) `REAL300004919663.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919663 none CC#CCC(NC(=O)C1=C(CC)N(CC(C)C)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 5, 8, 5, 5, 5, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 39, 11, 11, 1, 11, 1, 1, 1, 3, 1, 1, 3, 3, 3, 1, 1, 39, 58, 58, 90, 90, 90, 90, 90, 39, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1] 201 rigid atoms, others: [6, 8, 9, 10, 43, 12, 13, 17, 18] set([0, 1, 2, 3, 4, 5, 7, 11, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 455 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919663 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919663 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919663/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919663 Building REAL300004919664 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919664' /scratch/stefan/7775247/working/building/REAL300004919664 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919664 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919664/0 /scratch/stefan/7775247/working/building/REAL300004919664 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/668 `/scratch/stefan/7775247/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(C2=CC=CC(Cl)=C2F)N=N1)C(=O)[O-]) `REAL300004919664.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919664 none CC#CCC(NC(=O)C1=CN(C2=CC=CC(Cl)=C2F)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 15, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 44, 13, 13, 1, 13, 1, 1, 1, 1, 9, 9, 5, 9, 9, 9, 9, 1, 1, 44, 69, 69, 112, 112, 112, 112, 112, 44, 13, 1, 9, 9, 8] 201 rigid atoms, others: [6, 8, 9, 10, 11, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919664 none CC#CCC(NC(=O)C1=CN(C2=CC=CC(Cl)=C2F)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 15, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 123, 55, 55, 9, 55, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 123, 154, 154, 201, 201, 201, 201, 201, 123, 55, 9, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 916 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919664 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919664 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919664/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919664 Building REAL300004919665 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919665' /scratch/stefan/7775247/working/building/REAL300004919665 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919665 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919665/0 /scratch/stefan/7775247/working/building/REAL300004919665 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 669) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/669 `/scratch/stefan/7775247/working/3D/669' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=C(F)C=C2C)C=C1)C(=O)[O-]) `REAL300004919665.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919665 none CC#CCC(NC(=O)C1=NN(C2=CC=C(F)C=C2C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 35, 11, 11, 1, 11, 1, 1, 1, 1, 9, 9, 1, 1, 9, 9, 9, 1, 1, 35, 51, 51, 83, 83, 83, 83, 83, 35, 11, 9, 9, 9, 9, 9, 9, 1, 1] 159 rigid atoms, others: [37, 6, 8, 9, 10, 11, 19, 20, 38] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 409 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919665 none CC#CCC(NC(=O)C1=NN(C2=CC=C(F)C=C2C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [159, 159, 159, 98, 43, 43, 9, 43, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 98, 126, 126, 159, 159, 159, 159, 159, 98, 43, 1, 1, 1, 2, 2, 2, 9, 9] 159 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 741 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919665 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919665 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919665/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919665 Building REAL300004919666 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919666' /scratch/stefan/7775247/working/building/REAL300004919666 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919666 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919666/0 /scratch/stefan/7775247/working/building/REAL300004919666 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/670 `/scratch/stefan/7775247/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CC=CC(C(C)C)=C2)O1)C(=O)[O-]) `REAL300004919666.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919666 none CC#CCC(NC(=O)C1=CC=C(C2=CC=CC(C(C)C)=C2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 6, 5, 1, 5, 1, 1, 1, 1, 1, 13, 13, 1, 13, 13, 25, 25, 13, 1, 13, 23, 23, 32, 32, 32, 32, 32, 13, 6, 1, 1, 13, 13, 1, 25, 25, 25, 25, 25, 25, 25, 13] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) 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: REAL300004919666 none CC#CCC(NC(=O)C1=CC=C(C2=CC=CC(C(C)C)=C2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [156, 156, 156, 85, 36, 36, 13, 36, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 13, 85, 132, 132, 156, 156, 156, 156, 156, 85, 36, 13, 13, 1, 1, 1, 2, 3, 3, 3, 2, 2, 2, 1] 201 rigid atoms, others: [34, 35, 36, 44, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 824 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919666 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919666 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919666/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919666 Building REAL300004919667 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919667' /scratch/stefan/7775247/working/building/REAL300004919667 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919667 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919667/0 /scratch/stefan/7775247/working/building/REAL300004919667 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 671) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/671 `/scratch/stefan/7775247/working/3D/671' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(CC)C(S(C)(=O)=O)=C1)C(=O)[O-]) `REAL300004919667.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919667 none CC#CCC(NC(=O)C1=CC=C(CC)C(S(C)(=O)=O)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 5, 5, 1, 14, 5, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 6, 1, 1, 7, 7, 7, 1, 17, 30, 30, 72, 72, 72, 72, 72, 17, 5, 1, 1, 6, 6, 6, 6, 6, 7, 7, 7, 1] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 14, 15, 40, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 360 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919667 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919667 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919667/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919667 Building REAL300004919668 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919668' /scratch/stefan/7775247/working/building/REAL300004919668 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919668 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919668/0 /scratch/stefan/7775247/working/building/REAL300004919668 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/672 `/scratch/stefan/7775247/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC2=C1OCC(=O)N2)C(=O)[O-]) `REAL300004919668.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919668 none CC#CCC(NC(=O)C1=CC=CC2=C1OCC(=O)N2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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', 'N.am', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 36, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 50, 50, 86, 86, 86, 86, 86, 36, 12, 1, 1, 1, 1, 1, 1] 86 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 396 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919668 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919668 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919668/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919668 Building REAL300004919669 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919669' /scratch/stefan/7775247/working/building/REAL300004919669 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919669 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919669/0 /scratch/stefan/7775247/working/building/REAL300004919669 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 673) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/673 `/scratch/stefan/7775247/working/3D/673' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=C(S(=O)(=O)C(C)C)C=C1)C(=O)[O-]) `REAL300004919669.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919669 none CC#CCC(NC(=O)CC1=CC=C(S(=O)(=O)C(C)C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 27, 9, 9, 3, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 15, 15, 1, 1, 27, 41, 41, 74, 74, 74, 74, 74, 27, 9, 3, 3, 1, 1, 15, 15, 15, 15, 15, 15, 15, 1, 1] 201 rigid atoms, others: [33, 34, 43, 8, 9, 10, 11, 12, 13, 19, 20, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 408 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919669 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919669 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919669/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919669 Building REAL300004919670 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919670' /scratch/stefan/7775247/working/building/REAL300004919670 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919670 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919670/0 /scratch/stefan/7775247/working/building/REAL300004919670 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/674 `/scratch/stefan/7775247/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(Br)C=CO1)C(=O)[O-]) `REAL300004919670.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919670 none CC#CCC(NC(=O)C1=C(Br)C=CO1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 17, 1, 1, 12, 1, 11, 11, 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, 3, 7, 2, 2, 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: [43, 43, 43, 22, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 22, 34, 34, 43, 43, 43, 43, 43, 22, 5, 1, 1] 59 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 24, 25] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919670 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919670 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919670/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919670 Building REAL300004919671 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919671' /scratch/stefan/7775247/working/building/REAL300004919671 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919671 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919671/0 /scratch/stefan/7775247/working/building/REAL300004919671 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 675) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/675 `/scratch/stefan/7775247/working/3D/675' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=CC3=CC=CN=C3C=C2)N=N1)C(=O)[O-]) `REAL300004919671.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919671 none CC#CCC(NC(=O)C1=C(C)N(C2=CC3=CC=CN=C3C=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 37, 12, 12, 1, 12, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 37, 48, 48, 66, 66, 66, 66, 66, 37, 12, 2, 2, 2, 6, 6, 6, 6, 6, 6] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 22, 23] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 324 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: REAL300004919671 none CC#CCC(NC(=O)C1=C(C)N(C2=CC3=CC=CN=C3C=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 126, 45, 45, 6, 45, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 126, 159, 159, 201, 201, 201, 201, 201, 126, 45, 6, 6, 6, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 963 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919671 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919671 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919671/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919671 Building REAL300004919672 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919672' /scratch/stefan/7775247/working/building/REAL300004919672 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919672 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919672/0 /scratch/stefan/7775247/working/building/REAL300004919672 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/676 `/scratch/stefan/7775247/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC3=CN=CC=C32)N=N1)C(=O)[O-]) `REAL300004919672.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919672 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC3=CN=CC=C32)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 38, 12, 12, 1, 12, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 38, 59, 59, 94, 94, 94, 94, 94, 38, 13, 2, 2, 2, 7, 7, 7, 7, 7, 7] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 22, 23] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 475 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: REAL300004919672 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC3=CN=CC=C32)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 8, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 127, 54, 54, 7, 54, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 127, 161, 161, 201, 201, 201, 201, 201, 127, 54, 7, 7, 7, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 961 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919672 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919672 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919672/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919672 Building REAL300004919673 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919673' /scratch/stefan/7775247/working/building/REAL300004919673 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919673 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919673/0 /scratch/stefan/7775247/working/building/REAL300004919673 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 677) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/677 `/scratch/stefan/7775247/working/3D/677' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC3=NC=CC=C32)N=N1)C(=O)[O-]) `REAL300004919673.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919673 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC3=NC=CC=C32)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 8, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 37, 11, 11, 1, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 37, 61, 61, 94, 94, 94, 94, 94, 37, 12, 2, 2, 2, 7, 7, 7, 7, 7, 7] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 22, 23] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 488 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: REAL300004919673 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC3=NC=CC=C32)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 8, 8, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 127, 53, 53, 7, 53, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 127, 161, 161, 201, 201, 201, 201, 201, 127, 53, 7, 7, 7, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 971 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919673 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919673 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919673/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919673 Building REAL300004919674 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919674' /scratch/stefan/7775247/working/building/REAL300004919674 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919674 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919674/0 /scratch/stefan/7775247/working/building/REAL300004919674 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/678 `/scratch/stefan/7775247/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC3=CC=CN=C32)N=N1)C(=O)[O-]) `REAL300004919674.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919674 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC3=CC=CN=C32)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 38, 12, 12, 1, 12, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 38, 56, 56, 84, 84, 84, 84, 84, 38, 13, 2, 2, 2, 7, 7, 7, 7, 7, 7] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 22, 23] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 424 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: REAL300004919674 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC3=CC=CN=C32)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 8, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 122, 50, 50, 7, 50, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 122, 156, 156, 201, 201, 201, 201, 201, 122, 50, 7, 7, 7, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 956 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919674 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919674 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919674/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919674 Building REAL300004919675 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919675' /scratch/stefan/7775247/working/building/REAL300004919675 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919675 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919675/0 /scratch/stefan/7775247/working/building/REAL300004919675 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 679) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/679 `/scratch/stefan/7775247/working/3D/679' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(NC(C)=O)=CC=C1Cl)C(=O)[O-]) `REAL300004919675.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919675 none CC#CCC(NC(=O)C1=CC(NC(C)=O)=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 5, 11, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 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: [76, 76, 76, 26, 7, 7, 1, 7, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 26, 40, 40, 76, 76, 76, 76, 76, 26, 7, 1, 5, 5, 5, 5, 1, 1] 183 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 354 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919675 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919675 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919675/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919675 Building REAL300004919676 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919676' /scratch/stefan/7775247/working/building/REAL300004919676 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919676 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919676/0 /scratch/stefan/7775247/working/building/REAL300004919676 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/680 `/scratch/stefan/7775247/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NC=CC=C1C(F)(F)F)C(=O)[O-]) `REAL300004919676.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919676 none CC#CCC(NC(=O)C1=NC=CC=C1C(F)(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 14, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 22, 22, 40, 40, 40, 40, 40, 14, 6, 1, 1, 1] 40 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919676 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919676 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919676/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919676 Building REAL300004919677 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919677' /scratch/stefan/7775247/working/building/REAL300004919677 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919677 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919677/0 /scratch/stefan/7775247/working/building/REAL300004919677 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 681) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/681 `/scratch/stefan/7775247/working/3D/681' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=C([N+](=O)[O-])C=C1Cl)C(=O)[O-]) `REAL300004919677.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919677 none CC#CCC(NC(=O)CC1=CC=C([N+](=O)[O-])C=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 94, 39, 39, 6, 39, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 94, 141, 141, 201, 201, 201, 201, 201, 94, 39, 6, 6, 1, 1, 1] 201 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 1019 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919677 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919677 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919677/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919677 Building REAL300004919678 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919678' /scratch/stefan/7775247/working/building/REAL300004919678 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919678 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919678/0 /scratch/stefan/7775247/working/building/REAL300004919678 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/682 `/scratch/stefan/7775247/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCNC1=NC=C(C(F)(F)F)C=C1Cl)C(=O)[O-]) `REAL300004919678.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919678 none CC#CCC(NC(=O)CCNC1=NC=C(C(F)(F)F)C=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 1, 1, 5, 15, 15, 15, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 166, 117, 116, 32, 117, 23, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 170, 190, 190, 201, 201, 201, 201, 200, 170, 116, 32, 32, 23, 23, 3, 1, 1] 201 rigid atoms, others: [37, 38, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 907 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919678 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919678 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919678/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919678 Building REAL300004919679 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919679' /scratch/stefan/7775247/working/building/REAL300004919679 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919679 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919679/0 /scratch/stefan/7775247/working/building/REAL300004919679 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 683) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/683 `/scratch/stefan/7775247/working/3D/683' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN=C(OCC)C(Cl)=C1)C(=O)[O-]) `REAL300004919679.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919679 none CC#CCC(NC(=O)C1=CN=C(OCC)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 5, 5, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 8, 31, 1, 1, 1, 21, 36, 36, 79, 79, 79, 79, 79, 21, 7, 1, 31, 31, 31, 31, 31, 1] 201 rigid atoms, others: [34, 6, 8, 9, 10, 11, 12, 15, 16, 17, 28] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 452 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919679 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919679 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919679/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919679 Building REAL300004919680 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919680' /scratch/stefan/7775247/working/building/REAL300004919680 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919680 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919680/0 /scratch/stefan/7775247/working/building/REAL300004919680 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/684 `/scratch/stefan/7775247/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(OC2=CN=CC=N2)=C1)C(=O)[O-]) `REAL300004919680.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919680 none CC#CCC(NC(=O)C1=CC=CC(OC2=CN=CC=N2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 12, 1, 1, 8, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 18, 18, 18, 18, 18, 1, 13, 19, 19, 26, 26, 26, 26, 26, 13, 5, 1, 1, 1, 18, 18, 18, 1] 201 rigid atoms, others: [32, 33, 37, 6, 8, 9, 10, 11, 12, 13, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919680 none CC#CCC(NC(=O)C1=CC=CC(OC2=CN=CC=N2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 12, 1, 1, 8, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 106, 58, 58, 18, 58, 18, 18, 18, 18, 8, 1, 1, 1, 1, 1, 1, 1, 18, 106, 143, 143, 201, 201, 201, 201, 201, 106, 58, 18, 18, 18, 1, 1, 1, 18] 201 rigid atoms, others: [34, 35, 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, 37]) total number of confs: 967 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919680 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919680 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919680/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919680 Building REAL300004919681 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919681' /scratch/stefan/7775247/working/building/REAL300004919681 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919681 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919681/0 /scratch/stefan/7775247/working/building/REAL300004919681 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 685) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/685 `/scratch/stefan/7775247/working/3D/685' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)OC(C2=CC=CC=C2F)=N1)C(=O)[O-]) `REAL300004919681.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919681 none CC#CCC(NC(=O)C1=C(C)OC(C2=CC=CC=C2F)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 15, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [73, 73, 73, 31, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 13, 13, 1, 13, 13, 13, 1, 31, 50, 50, 73, 73, 73, 73, 73, 31, 11, 2, 2, 2, 13, 13, 12, 13] 169 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 20] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919681 none CC#CCC(NC(=O)C1=C(C)OC(C2=CC=CC=C2F)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 15, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [169, 169, 169, 108, 53, 53, 13, 52, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 13, 108, 141, 141, 169, 169, 169, 169, 169, 108, 53, 13, 13, 13, 1, 1, 1, 1] 169 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 805 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919681 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919681 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919681/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919681 Building REAL300004919682 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919682' /scratch/stefan/7775247/working/building/REAL300004919682 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919682 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919682/0 /scratch/stefan/7775247/working/building/REAL300004919682 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/686 `/scratch/stefan/7775247/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(C(=O)N2CCCC2)=N1)C(=O)[O-]) `REAL300004919682.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919682 none CC#CCC(NC(=O)C1=CC=CC(C(=O)N2CCCC2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 2, 2, 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: [86, 86, 86, 31, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 14, 14, 14, 14, 1, 31, 50, 50, 86, 86, 86, 86, 86, 31, 11, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14] 172 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 443 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919682 none CC#CCC(NC(=O)C1=CC=CC(C(=O)N2CCCC2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 2, 2, 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, 172, 99, 51, 51, 14, 51, 14, 14, 14, 14, 5, 1, 5, 1, 1, 1, 1, 1, 14, 99, 133, 133, 172, 172, 172, 172, 172, 99, 51, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1] 172 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 13, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 827 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919682 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919682 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919682/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919682 Building REAL300004919683 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919683' /scratch/stefan/7775247/working/building/REAL300004919683 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919683 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919683/0 /scratch/stefan/7775247/working/building/REAL300004919683 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 687) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/687 `/scratch/stefan/7775247/working/3D/687' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC(=O)C1=CC(C)=CC=C1C)C(=O)[O-]) `REAL300004919683.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919683 none CC#CCC(NC(=O)CCC(=O)C1=CC(C)=CC=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 1, 11, 1, 1, 1, 5, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 121, 121, 55, 121, 35, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 170, 194, 194, 201, 201, 201, 201, 201, 170, 121, 55, 55, 35, 35, 1, 2, 2, 2, 1, 1, 2, 2, 2] 201 rigid atoms, others: [34, 38, 39, 10, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 40, 41, 42]) total number of confs: 996 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919683 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919683 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919683/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919683 Building REAL300004919684 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919684' /scratch/stefan/7775247/working/building/REAL300004919684 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919684 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919684/0 /scratch/stefan/7775247/working/building/REAL300004919684 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/688 `/scratch/stefan/7775247/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC(=O)C1=CC=C(CC)C=C1)C(=O)[O-]) `REAL300004919684.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919684 none CC#CCC(NC(=O)CCC(=O)C1=CC=C(CC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 1, 11, 1, 1, 1, 1, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 55, 41, 41, 23, 41, 20, 7, 1, 7, 1, 1, 1, 1, 1, 2, 1, 1, 55, 55, 55, 69, 69, 69, 69, 69, 55, 41, 23, 23, 20, 20, 1, 1, 2, 2, 3, 3, 3, 1, 1] 135 rigid atoms, others: [34, 35, 41, 10, 12, 13, 14, 15, 16, 18, 19, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40]) total number of confs: 324 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919684 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919684 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919684/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919684 Building REAL300004919685 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919685' /scratch/stefan/7775247/working/building/REAL300004919685 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919685 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919685/0 /scratch/stefan/7775247/working/building/REAL300004919685 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 689) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/689 `/scratch/stefan/7775247/working/3D/689' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC(=O)C1=C(C)SC(C)=C1)C(=O)[O-]) `REAL300004919685.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919685 none CC#CCC(NC(=O)CCC(=O)C1=C(C)SC(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 5, 1, 11, 1, 1, 5, 14, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 114, 113, 57, 114, 36, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 156, 189, 189, 201, 201, 201, 201, 201, 156, 113, 57, 57, 36, 36, 2, 2, 2, 2, 2, 2, 1] 201 rigid atoms, others: [39, 10, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 1024 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919685 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919685 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919685/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919685 Building REAL300004919686 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919686' /scratch/stefan/7775247/working/building/REAL300004919686 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919686 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919686/0 /scratch/stefan/7775247/working/building/REAL300004919686 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/690 `/scratch/stefan/7775247/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CC(=O)N(C2=CC=C(OC)C=C2OC)C1)C(=O)[O-]) `REAL300004919686.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919686 none CC#CCC(NC(=O)C1CC(=O)N(C2=CC=C(OC)C=C2OC)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 30, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 9, 6, 6, 6, 8, 1, 30, 53, 53, 73, 73, 73, 73, 73, 30, 10, 1, 1, 1, 6, 6, 9, 9, 9, 6, 8, 8, 8, 1, 1] 201 rigid atoms, others: [34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 46, 47, 23] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 409 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: REAL300004919686 none CC#CCC(NC(=O)C1CC(=O)N(C2=CC=C(OC)C=C2OC)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 53, 22, 22, 6, 22, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 4, 6, 53, 89, 89, 118, 118, 118, 118, 118, 53, 22, 6, 6, 6, 1, 1, 3, 3, 3, 1, 4, 4, 4, 6, 6] 201 rigid atoms, others: [37, 38, 42, 12, 13, 14, 15, 16, 17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 43, 44, 45, 46, 47]) total number of confs: 629 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919686 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919686 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919686/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919686 Building REAL300004919687 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919687' /scratch/stefan/7775247/working/building/REAL300004919687 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919687 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919687/0 /scratch/stefan/7775247/working/building/REAL300004919687 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 691) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/691 `/scratch/stefan/7775247/working/3D/691' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC(=O)C1=CC=C2CCCC2=C1)C(=O)[O-]) `REAL300004919687.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919687 none CC#CCC(NC(=O)CCC(=O)C1=CC=C2CCCC2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 1, 11, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 126, 125, 54, 126, 39, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 164, 195, 195, 201, 201, 201, 201, 201, 164, 125, 54, 54, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 1010 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919687 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919687 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919687/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919687 Building REAL300004919688 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919688' /scratch/stefan/7775247/working/building/REAL300004919688 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919688 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919688/0 /scratch/stefan/7775247/working/building/REAL300004919688 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/692 `/scratch/stefan/7775247/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC(OC)=CC=C1OC)C(=O)[O-]) `REAL300004919688.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919688 none CC#CCC(NC(=O)CC1=CC(OC)=CC=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 12, 5, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [148, 148, 148, 64, 33, 33, 6, 33, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 3, 64, 98, 98, 148, 148, 148, 148, 148, 64, 33, 6, 6, 1, 3, 3, 3, 1, 1, 3, 3, 3] 201 rigid atoms, others: [35, 36, 8, 9, 10, 11, 12, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 37, 38, 39]) total number of confs: 751 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919688 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919688 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919688/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919688 Building REAL300004919689 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919689' /scratch/stefan/7775247/working/building/REAL300004919689 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919689 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919689/0 /scratch/stefan/7775247/working/building/REAL300004919689 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 693) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/693 `/scratch/stefan/7775247/working/3D/693' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C2=CC=CC=C2)N=C(C)S1)C(=O)[O-]) `REAL300004919689.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919689 none CC#CCC(NC(=O)C1=C(C2=CC=CC=C2)N=C(C)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [138, 138, 138, 53, 13, 13, 1, 13, 1, 1, 1, 6, 6, 1, 6, 6, 1, 1, 1, 1, 53, 81, 81, 138, 138, 138, 138, 138, 53, 13, 6, 6, 1, 6, 6, 2, 2, 2] 163 rigid atoms, others: [6, 8, 9, 10, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 653 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919689 none CC#CCC(NC(=O)C1=C(C2=CC=CC=C2)N=C(C)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [163, 163, 163, 90, 36, 36, 6, 36, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 90, 119, 119, 163, 163, 163, 163, 163, 90, 36, 1, 1, 1, 1, 1, 6, 6, 6] 163 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37]) total number of confs: 760 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919689 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919689 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919689/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919689 Building REAL300004919690 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919690' /scratch/stefan/7775247/working/building/REAL300004919690 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919690 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919690/0 /scratch/stefan/7775247/working/building/REAL300004919690 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/694 `/scratch/stefan/7775247/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC(=O)C1=CC=C(OC)C=C1)C(=O)[O-]) `REAL300004919690.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919690 none CC#CCC(NC(=O)CCC(=O)C1=CC=C(OC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 5, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 69, 48, 48, 22, 48, 20, 7, 1, 7, 1, 1, 1, 1, 1, 2, 1, 1, 69, 69, 69, 99, 99, 99, 99, 99, 69, 48, 22, 22, 20, 20, 1, 1, 3, 3, 3, 1, 1] 99 rigid atoms, others: [34, 35, 39, 40, 10, 12, 13, 14, 15, 16, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 450 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919690 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919690 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919690/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919690 Building REAL300004919691 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919691' /scratch/stefan/7775247/working/building/REAL300004919691 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919691 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919691/0 /scratch/stefan/7775247/working/building/REAL300004919691 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 695) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/695 `/scratch/stefan/7775247/working/3D/695' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC(=O)C1=CC=C(OC)C(F)=C1)C(=O)[O-]) `REAL300004919691.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919691 none CC#CCC(NC(=O)CCC(=O)C1=CC=C(OC)C(F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 1, 11, 1, 1, 1, 1, 12, 5, 1, 15, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 183, 109, 72, 72, 22, 72, 19, 9, 1, 9, 1, 1, 1, 1, 1, 3, 1, 1, 1, 110, 143, 143, 183, 183, 183, 183, 183, 110, 72, 22, 22, 19, 19, 1, 1, 4, 4, 4, 1] 201 rigid atoms, others: [35, 36, 40, 10, 12, 13, 14, 15, 16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39]) total number of confs: 957 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919691 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919691 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919691/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919691 Building REAL300004919692 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919692' /scratch/stefan/7775247/working/building/REAL300004919692 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919692 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919692/0 /scratch/stefan/7775247/working/building/REAL300004919692 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/696 `/scratch/stefan/7775247/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=CC=C(Br)C=C2C=C1)C(=O)[O-]) `REAL300004919692.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919692 none CC#CCC(NC(=O)C1=CC2=CC=C(Br)C=C2C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 29, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 39, 39, 67, 67, 67, 67, 67, 29, 7, 1, 1, 1, 1, 1, 1] 67 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919692 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919692 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919692/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919692 Building REAL300004919693 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919693' /scratch/stefan/7775247/working/building/REAL300004919693 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919693 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919693/0 /scratch/stefan/7775247/working/building/REAL300004919693 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 697) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/697 `/scratch/stefan/7775247/working/3D/697' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(OC(C)C)C=C1)C(=O)[O-]) `REAL300004919693.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919693 none CC#CCC(NC(=O)C=CC1=CC=C(OC(C)C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 34, 16, 16, 3, 16, 3, 1, 1, 1, 1, 1, 1, 7, 16, 16, 1, 1, 34, 54, 54, 75, 75, 75, 75, 75, 34, 16, 3, 3, 1, 1, 16, 16, 16, 16, 16, 16, 16, 1, 1] 201 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 18, 19, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 430 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919693 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919693 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919693/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919693 Building REAL300004919694 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919694' /scratch/stefan/7775247/working/building/REAL300004919694 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919694 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919694/0 /scratch/stefan/7775247/working/building/REAL300004919694 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/698 `/scratch/stefan/7775247/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CC(=O)N(C2=CC=C(CCC)C=C2)C1)C(=O)[O-]) `REAL300004919694.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919694 none CC#CCC(NC(=O)C1CC(=O)N(C2=CC=C(CCC)C=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 1, 11, 8, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 23, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1, 7, 11, 4, 4, 1, 23, 40, 40, 59, 59, 59, 59, 59, 23, 9, 1, 1, 1, 4, 4, 7, 7, 11, 11, 11, 11, 11, 4, 4, 1, 1] 201 rigid atoms, others: [33, 34, 35, 6, 48, 8, 9, 10, 11, 12, 13, 47, 22] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 354 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919694 none CC#CCC(NC(=O)C1CC(=O)N(C2=CC=C(CCC)C=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 1, 11, 8, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 98, 48, 23, 23, 4, 23, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 2, 6, 1, 1, 4, 48, 72, 72, 98, 98, 98, 98, 98, 48, 23, 4, 4, 4, 1, 1, 2, 2, 6, 6, 7, 7, 7, 1, 1, 4, 4] 201 rigid atoms, others: [45, 36, 37, 46, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 523 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919694 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919694 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919694/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919694 Building REAL300004919695 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919695' /scratch/stefan/7775247/working/building/REAL300004919695 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919695 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919695/0 /scratch/stefan/7775247/working/building/REAL300004919695 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 699) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/699 `/scratch/stefan/7775247/working/3D/699' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2[N+](=O)[O-])C=C1)C(=O)[O-]) `REAL300004919695.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919695 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2[N+](=O)[O-])C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 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: [89, 89, 89, 34, 11, 11, 1, 11, 1, 1, 1, 1, 7, 7, 1, 7, 7, 7, 7, 7, 1, 1, 34, 48, 48, 89, 89, 89, 89, 89, 34, 11, 7, 7, 1, 7, 1, 1] 152 rigid atoms, others: [36, 37, 6, 8, 9, 10, 11, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 400 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919695 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2[N+](=O)[O-])C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [152, 152, 152, 77, 34, 34, 7, 34, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 7, 77, 102, 102, 152, 152, 152, 152, 152, 77, 34, 1, 1, 1, 1, 7, 7] 152 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37]) total number of confs: 709 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919695 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919695 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919695/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919695 Building REAL300004919696 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919696' /scratch/stefan/7775247/working/building/REAL300004919696 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919696 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919696/0 /scratch/stefan/7775247/working/building/REAL300004919696 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/700 `/scratch/stefan/7775247/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCC(=O)C1=CC=C(OC)C=C1)C(=O)[O-]) `REAL300004919696.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919696 none CC#CCC(NC(=O)CCCC(=O)C1=CC=C(OC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [194, 194, 194, 141, 119, 119, 56, 119, 30, 24, 6, 1, 6, 1, 1, 1, 1, 1, 2, 1, 1, 141, 150, 150, 194, 194, 194, 194, 194, 141, 119, 54, 56, 33, 33, 24, 24, 1, 1, 3, 3, 3, 1, 1] 201 rigid atoms, others: [43, 37, 38, 42, 11, 13, 14, 15, 16, 17, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 917 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919696 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919696 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919696/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919696 Building REAL300004919697 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919697' /scratch/stefan/7775247/working/building/REAL300004919697 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919697 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919697/0 /scratch/stefan/7775247/working/building/REAL300004919697 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 701) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/701 `/scratch/stefan/7775247/working/3D/701' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Br)=C2OCOC2=C1)C(=O)[O-]) `REAL300004919697.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919697 none CC#CCC(NC(=O)C1=CC(Br)=C2OCOC2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 17, 1, 12, 5, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 37, 37, 70, 70, 70, 70, 70, 25, 7, 1, 1, 1, 1] 70 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 321 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919697 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919697 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919697/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919697 Building REAL300004919698 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919698' /scratch/stefan/7775247/working/building/REAL300004919698 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919698 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919698/0 /scratch/stefan/7775247/working/building/REAL300004919698 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/702 `/scratch/stefan/7775247/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C(=O)N(CC)CC)C=C1)C(=O)[O-]) `REAL300004919698.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919698 none CC#CCC(NC(=O)C1=CC=C(C(=O)N(CC)CC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 7, 7, 11, 18, 11, 14, 1, 1, 9, 16, 16, 37, 37, 37, 37, 37, 9, 3, 1, 1, 18, 18, 18, 18, 18, 14, 14, 14, 14, 14, 1, 1] 201 rigid atoms, others: [32, 43, 6, 8, 9, 10, 11, 12, 44, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 253 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919698 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919698 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919698/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919698 Building REAL300004919699 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919699' /scratch/stefan/7775247/working/building/REAL300004919699 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919699 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919699/0 /scratch/stefan/7775247/working/building/REAL300004919699 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 703) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/703 `/scratch/stefan/7775247/working/3D/703' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCCOC1=CC=C(Br)C=C1)C(=O)[O-]) `REAL300004919699.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919699 none CC#CCC(NC(=O)CCCCOC1=CC=C(Br)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 132, 132, 36, 132, 15, 14, 6, 4, 1, 1, 1, 1, 1, 1, 1, 1, 153, 159, 159, 201, 201, 201, 201, 201, 153, 132, 36, 36, 15, 15, 14, 14, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 813 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919699 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919699 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919699/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919699 Building REAL300004919700 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919700' /scratch/stefan/7775247/working/building/REAL300004919700 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919700 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919700/0 /scratch/stefan/7775247/working/building/REAL300004919700 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/704 `/scratch/stefan/7775247/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CC)C1=CC=C(OC)C=C1)C(=O)[O-]) `REAL300004919700.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919700 none CC#CCC(NC(=O)C(CC)C1=CC=C(OC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 133, 61, 23, 23, 7, 23, 1, 7, 10, 1, 1, 1, 1, 1, 2, 1, 1, 61, 98, 98, 133, 133, 133, 133, 133, 61, 23, 7, 10, 10, 10, 10, 10, 1, 1, 3, 3, 3, 1, 1] 201 rigid atoms, others: [35, 36, 8, 41, 11, 12, 13, 14, 15, 17, 18, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39]) total number of confs: 724 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919700 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919700 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919700/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919700 Building REAL300004919701 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919701' /scratch/stefan/7775247/working/building/REAL300004919701 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919701 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919701/0 /scratch/stefan/7775247/working/building/REAL300004919701 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 705) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/705 `/scratch/stefan/7775247/working/3D/705' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Cl)=CC=C1OCCOC)C(=O)[O-]) `REAL300004919701.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919701 none CC#CCC(NC(=O)C1=CC(Cl)=CC=C1OCCOC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 12, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 9, 35, 55, 88, 15, 23, 23, 38, 38, 38, 38, 38, 15, 7, 1, 1, 1, 35, 35, 55, 55, 88, 88, 88] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 462 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919701 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919701 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919701/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919701 Building REAL300004919702 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919702' /scratch/stefan/7775247/working/building/REAL300004919702 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919702 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919702/0 /scratch/stefan/7775247/working/building/REAL300004919702 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/706 `/scratch/stefan/7775247/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CC12CCS(=O)(=O)CC2)C(=O)[O-]) `REAL300004919702.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919702 none CC#CCC(NC(=O)C1CC12CCS(=O)(=O)CC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 5, 14, 11, 11, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 30, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 43, 43, 68, 68, 68, 68, 68, 30, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 68 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 308 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919702 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919702 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919702/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919702 Building REAL300004919703 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919703' /scratch/stefan/7775247/working/building/REAL300004919703 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919703 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919703/0 /scratch/stefan/7775247/working/building/REAL300004919703 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 707) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/707 `/scratch/stefan/7775247/working/3D/707' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(Cl)C=C1SCC)C(=O)[O-]) `REAL300004919703.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919703 none CC#CCC(NC(=O)C1=CC=C(Cl)C=C1SCC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 14, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 31, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 9, 30, 31, 48, 48, 85, 85, 85, 85, 85, 31, 11, 1, 1, 1, 30, 30, 31, 31, 31] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35]) total number of confs: 493 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919703 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919703 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919703/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919703 Building REAL300004919704 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919704' /scratch/stefan/7775247/working/building/REAL300004919704 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919704 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919704/0 /scratch/stefan/7775247/working/building/REAL300004919704 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/708 `/scratch/stefan/7775247/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)(C)C1=CC=C(OCC)C(OCC)=C1)C(=O)[O-]) `REAL300004919704.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919704 none CC#CCC(NC(=O)C(C)(C)C1=CC=C(OCC)C(OCC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 12, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 31, 17, 17, 9, 17, 1, 9, 9, 1, 1, 1, 1, 1, 9, 13, 1, 1, 9, 19, 1, 31, 47, 47, 58, 58, 58, 58, 58, 31, 17, 9, 9, 9, 9, 9, 9, 1, 1, 13, 13, 14, 14, 14, 19, 19, 19, 19, 19, 1] 201 rigid atoms, others: [51, 39, 8, 11, 12, 13, 14, 15, 40, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 16, 17, 20, 21, 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]) total number of confs: 402 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919704 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919704 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919704/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919704 Building REAL300004919705 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919705' /scratch/stefan/7775247/working/building/REAL300004919705 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919705 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919705/0 /scratch/stefan/7775247/working/building/REAL300004919705 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 709) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/709 `/scratch/stefan/7775247/working/3D/709' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=CC(Br)=CC(C)=C2O1)C(=O)[O-]) `REAL300004919705.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919705 none CC#CCC(NC(=O)C1=CC2=CC(Br)=CC(C)=C2O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 17, 1, 1, 5, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 36, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 48, 48, 63, 63, 63, 63, 63, 36, 12, 1, 1, 1, 2, 2, 2] 63 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 32, 34, 33, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 310 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919705 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919705 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919705/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919705 Building REAL300004919706 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919706' /scratch/stefan/7775247/working/building/REAL300004919706 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919706 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919706/0 /scratch/stefan/7775247/working/building/REAL300004919706 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/710 `/scratch/stefan/7775247/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC(Cl)=CC=C1Br)C(=O)[O-]) `REAL300004919706.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919706 none CC#CCC(NC(=O)CCC1=CC(Cl)=CC=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 16, 1, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 103, 49, 49, 10, 49, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 103, 138, 138, 201, 201, 201, 201, 201, 103, 49, 10, 10, 6, 6, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 966 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919706 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919706 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919706/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919706 Building REAL300004919707 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919707' /scratch/stefan/7775247/working/building/REAL300004919707 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919707 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919707/0 /scratch/stefan/7775247/working/building/REAL300004919707 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 711) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/711 `/scratch/stefan/7775247/working/3D/711' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)(C)C1=CC=C(CC)C=C1)C(=O)[O-]) `REAL300004919707.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919707 none CC#CCC(NC(=O)C(C)(C)C1=CC=C(CC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 110, 60, 28, 28, 7, 28, 1, 7, 7, 1, 1, 1, 1, 1, 3, 1, 1, 60, 79, 79, 110, 110, 110, 110, 110, 60, 28, 7, 7, 7, 7, 7, 7, 1, 1, 3, 3, 3, 3, 3, 1, 1] 201 rigid atoms, others: [35, 36, 8, 42, 11, 12, 13, 14, 15, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 16, 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: 536 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919707 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919707 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919707/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919707 Building REAL300004919708 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919708' /scratch/stefan/7775247/working/building/REAL300004919708 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919708 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919708/0 /scratch/stefan/7775247/working/building/REAL300004919708 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/712 `/scratch/stefan/7775247/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC)C=C1OC(C)C)C(=O)[O-]) `REAL300004919708.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919708/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919708 none CC#CCC(NC(=O)C1=CC=C(OC)C=C1OC(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 30, 12, 12, 1, 12, 1, 1, 1, 1, 1, 2, 1, 1, 1, 7, 17, 17, 30, 46, 46, 86, 86, 86, 86, 86, 30, 12, 1, 1, 2, 2, 2, 1, 17, 17, 17, 17, 17, 17, 17] 201 rigid atoms, others: [35, 6, 8, 9, 10, 11, 12, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 455 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919708 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919708 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919708/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919708 Building REAL300004919709 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919709' /scratch/stefan/7775247/working/building/REAL300004919709 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919709 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919709/0 /scratch/stefan/7775247/working/building/REAL300004919709 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 713) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/713 `/scratch/stefan/7775247/working/3D/713' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC)C=C1OCC1CC1)C(=O)[O-]) `REAL300004919709.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919709 none CC#CCC(NC(=O)C1=CC=C(OC)C=C1OCC1CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 8, 8, 1, 8, 1, 1, 1, 1, 1, 3, 1, 1, 1, 9, 32, 66, 66, 15, 24, 24, 38, 38, 38, 38, 38, 15, 8, 1, 1, 3, 3, 3, 1, 32, 32, 66, 66, 66, 66, 66] 201 rigid atoms, others: [32, 36, 6, 8, 9, 10, 11, 12, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 406 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919709 none CC#CCC(NC(=O)C1=CC=C(OC)C=C1OCC1CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 184, 184, 118, 89, 89, 66, 89, 66, 66, 66, 66, 66, 92, 66, 36, 8, 1, 1, 1, 1, 118, 145, 145, 184, 184, 184, 184, 184, 118, 89, 66, 66, 92, 92, 92, 66, 8, 8, 1, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 43, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 851 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919709 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919709 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919709/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919709 Building REAL300004919710 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919710' /scratch/stefan/7775247/working/building/REAL300004919710 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919710 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919710/0 /scratch/stefan/7775247/working/building/REAL300004919710 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/714 `/scratch/stefan/7775247/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC(CC)C1=CC=C(OC)C=C1)C(=O)[O-]) `REAL300004919710.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919710 none CC#CCC(NC(=O)CC(CC)C1=CC=C(OC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 98, 54, 28, 28, 6, 28, 2, 1, 2, 3, 1, 1, 1, 1, 1, 2, 1, 1, 54, 57, 57, 98, 98, 98, 98, 98, 54, 28, 6, 6, 2, 3, 3, 3, 3, 3, 1, 1, 2, 2, 2, 1, 1] 110 rigid atoms, others: [38, 39, 9, 43, 12, 13, 14, 15, 16, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 451 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919710 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919710 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919710/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919710 Building REAL300004919711 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919711' /scratch/stefan/7775247/working/building/REAL300004919711 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919711 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919711/0 /scratch/stefan/7775247/working/building/REAL300004919711 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 715) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/715 `/scratch/stefan/7775247/working/3D/715' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CSC(S(C)(=O)=O)=C1)C(=O)[O-]) `REAL300004919711.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919711 none CC#CCC(NC(=O)C1=CSC(S(C)(=O)=O)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 14, 5, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 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: [99, 99, 99, 29, 7, 7, 1, 7, 1, 1, 1, 1, 1, 6, 6, 6, 1, 29, 48, 48, 99, 99, 99, 99, 99, 29, 7, 1, 7, 7, 7, 1] 194 rigid atoms, others: [6, 8, 9, 10, 11, 12, 16, 27, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30]) total number of confs: 475 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919711 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919711 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919711/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919711 Building REAL300004919712 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919712' /scratch/stefan/7775247/working/building/REAL300004919712 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919712 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919712/0 /scratch/stefan/7775247/working/building/REAL300004919712 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/716 `/scratch/stefan/7775247/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN=C2C(=C1)C=NN2CC1=CC=CC=C1)C(=O)[O-]) `REAL300004919712.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919712 none CC#CCC(NC(=O)C1=CN=C2C(=C1)C=NN2CC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 14, 14, 14, 14, 14, 17, 27, 27, 47, 47, 47, 47, 47, 17, 5, 1, 1, 1, 7, 7, 14, 14, 14, 14, 14] 201 rigid atoms, others: [34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919712 none CC#CCC(NC(=O)C1=CN=C2C(=C1)C=NN2CC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 110, 45, 45, 14, 45, 14, 14, 14, 14, 14, 14, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 110, 144, 144, 201, 201, 201, 201, 201, 110, 45, 14, 14, 14, 4, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 988 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919712 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919712 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919712/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919712 Building REAL300004919713 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919713' /scratch/stefan/7775247/working/building/REAL300004919713 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919713 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919713/0 /scratch/stefan/7775247/working/building/REAL300004919713 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 717) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/717 `/scratch/stefan/7775247/working/3D/717' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN=C2C(=C1)C(=O)NC(=O)N2C1CC1)C(=O)[O-]) `REAL300004919713.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919713 none CC#CCC(NC(=O)C1=CN=C2C(=C1)C(=O)NC(=O)N2C1CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 11, 8, 1, 11, 8, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 2, 2, 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: [87, 87, 87, 30, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 30, 46, 46, 87, 87, 87, 87, 87, 30, 7, 1, 1, 1, 5, 5, 5, 5, 5] 145 rigid atoms, others: [33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40]) total number of confs: 398 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919713 none CC#CCC(NC(=O)C1=CN=C2C(=C1)C(=O)NC(=O)N2C1CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 11, 8, 1, 11, 8, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [145, 145, 145, 68, 20, 20, 5, 20, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 68, 93, 93, 145, 145, 145, 145, 145, 68, 20, 5, 5, 5, 1, 1, 1, 1, 1] 145 rigid atoms, others: [36, 37, 38, 39, 40, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 666 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919713 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919713 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919713/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919713 Building REAL300004919714 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919714' /scratch/stefan/7775247/working/building/REAL300004919714 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919714 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919714/0 /scratch/stefan/7775247/working/building/REAL300004919714 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/718 `/scratch/stefan/7775247/working/3D/718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN=C2C(=C1)C(C)=NN2C)C(=O)[O-]) `REAL300004919714.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919714 none CC#CCC(NC(=O)C1=CN=C2C(=C1)C(C)=NN2C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 5, 8, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 34, 34, 65, 65, 65, 65, 65, 24, 7, 1, 1, 2, 2, 2, 2, 2, 2] 65 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 307 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919714 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919714 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919714/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919714 Building REAL300004919715 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919715' /scratch/stefan/7775247/working/building/REAL300004919715 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919715 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919715/0 /scratch/stefan/7775247/working/building/REAL300004919715 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 719) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/719 `/scratch/stefan/7775247/working/3D/719' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(OCC2=NOC(C)=N2)=C1)C(=O)[O-]) `REAL300004919715.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919715 none CC#CCC(NC(=O)C1=CC=CC(OCC2=NOC(C)=N2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 1, 8, 12, 1, 5, 8, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 3, 3, 17, 17, 17, 17, 17, 1, 15, 26, 26, 36, 36, 36, 36, 36, 15, 5, 1, 1, 1, 3, 3, 17, 17, 17, 1] 201 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 40, 21] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919715 none CC#CCC(NC(=O)C1=CC=CC(OCC2=NOC(C)=N2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 1, 8, 12, 1, 5, 8, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 115, 51, 51, 17, 51, 17, 16, 17, 17, 8, 8, 1, 1, 1, 1, 1, 1, 1, 17, 115, 145, 145, 201, 201, 201, 201, 201, 115, 51, 16, 17, 17, 8, 8, 2, 2, 2, 17] 201 rigid atoms, others: [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]) total number of confs: 956 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919715 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919715 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919715/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919715 Building REAL300004919716 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919716' /scratch/stefan/7775247/working/building/REAL300004919716 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919716 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919716/0 /scratch/stefan/7775247/working/building/REAL300004919716 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/720 `/scratch/stefan/7775247/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C(F)(F)F)C=N1)C(=O)[O-]) `REAL300004919716.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919716 none CC#CCC(NC(=O)C1=CC=C(C(F)(F)F)C=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 25, 11, 11, 1, 11, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 25, 32, 32, 49, 49, 49, 49, 49, 25, 11, 1, 1, 1] 49 rigid atoms, others: [6, 8, 9, 10, 11, 12, 16, 17, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919716 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919716 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919716/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919716 Building REAL300004919717 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919717' /scratch/stefan/7775247/working/building/REAL300004919717 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004919717 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919717/0 /scratch/stefan/7775247/working/building/REAL300004919717 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 721) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/721 `/scratch/stefan/7775247/working/3D/721' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N=C(C(C)(C)C)NC1=O)C(=O)[O-]) `REAL300004919717.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919717 none CC#CCC(NC(=O)C1=C(C)N=C(C(C)(C)C)NC1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 8, 1, 5, 5, 5, 5, 8, 1, 11, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 2, 2, 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: [82, 82, 82, 38, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 38, 54, 54, 82, 82, 82, 82, 82, 38, 10, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1] 111 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 17, 18, 19, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 400 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919717 /scratch/stefan/7775247/working /scratch/stefan/7775247 mkdir: created directory `1' /scratch/stefan/7775247/working/building/REAL300004919717/1 /scratch/stefan/7775247/working/building/REAL300004919717 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 1 (index: 722) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/722 `/scratch/stefan/7775247/working/3D/722' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N=C(C(C)(C)C)[N-]C1=O)C(=O)[O-]) `REAL300004919717.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004919717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919717 none CC#CCC(NC(=O)C1=C(C)N=C(C(C)(C)C)[N-]C1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 8, 1, 5, 5, 5, 5, 8, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 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: [78, 78, 78, 33, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 33, 53, 53, 78, 78, 78, 78, 78, 33, 10, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4] 102 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 428 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919717 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919717 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 1: /scratch/stefan/7775247/working/building/REAL300004919717/1.* 0: /scratch/stefan/7775247/working/building/REAL300004919717/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919717 Building REAL300004919718 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919718' /scratch/stefan/7775247/working/building/REAL300004919718 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919718 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919718/0 /scratch/stefan/7775247/working/building/REAL300004919718 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 723) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/723 `/scratch/stefan/7775247/working/3D/723' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC=C(OC2=CC=CC=N2)C=C1)C(=O)[O-]) `REAL300004919718.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919718 none CC#CCC(NC(=O)COC1=CC=C(OC2=CC=CC=N2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 30, 19, 19, 10, 19, 4, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 17, 17, 1, 1, 30, 39, 39, 53, 53, 53, 53, 53, 30, 19, 10, 10, 1, 1, 17, 17, 17, 17, 1, 1] 201 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 21, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919718 none CC#CCC(NC(=O)COC1=CC=C(OC2=CC=CC=N2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 108, 108, 56, 108, 38, 17, 13, 17, 17, 8, 1, 1, 1, 1, 1, 1, 1, 17, 17, 151, 162, 162, 201, 201, 201, 201, 201, 151, 108, 56, 56, 17, 17, 1, 1, 1, 1, 17, 17] 201 rigid atoms, others: [37, 38, 39, 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, 41, 42]) total number of confs: 908 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919718 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919718 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919718/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919718 Building REAL300004919719 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919719' /scratch/stefan/7775247/working/building/REAL300004919719 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919719 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919719/0 /scratch/stefan/7775247/working/building/REAL300004919719 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/724 `/scratch/stefan/7775247/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NOC(C2=CC=CC(Cl)=C2)=C1)C(=O)[O-]) `REAL300004919719.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919719 none CC#CCC(NC(=O)C1=NOC(C2=CC=CC(Cl)=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 28, 10, 10, 1, 10, 1, 1, 1, 1, 1, 13, 13, 1, 13, 13, 13, 1, 28, 44, 44, 60, 60, 60, 60, 60, 28, 10, 13, 13, 12, 13, 1] 201 rigid atoms, others: [34, 6, 8, 9, 10, 11, 12, 19] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919719 none CC#CCC(NC(=O)C1=NOC(C2=CC=CC(Cl)=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 70, 71, 13, 71, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 13, 141, 163, 163, 201, 201, 201, 201, 201, 141, 71, 1, 1, 1, 1, 13] 201 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 888 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919719 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919719 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919719/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919719 Building REAL300004919720 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919720' /scratch/stefan/7775247/working/building/REAL300004919720 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919720 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919720/0 /scratch/stefan/7775247/working/building/REAL300004919720 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 725) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/725 `/scratch/stefan/7775247/working/3D/725' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C2=CC=CC=C2)ON=C1C)C(=O)[O-]) `REAL300004919720.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919720 none CC#CCC(NC(=O)C1=C(C2=CC=CC=C2)ON=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [151, 151, 151, 56, 13, 13, 1, 13, 1, 1, 1, 7, 7, 1, 7, 7, 1, 1, 1, 1, 56, 92, 92, 151, 151, 151, 151, 151, 56, 13, 7, 7, 1, 7, 7, 2, 2, 2] 198 rigid atoms, others: [6, 8, 9, 10, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 756 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: REAL300004919720 none CC#CCC(NC(=O)C1=C(C2=CC=CC=C2)ON=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [198, 198, 198, 110, 43, 43, 7, 43, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 110, 146, 146, 198, 198, 198, 198, 198, 110, 43, 1, 1, 1, 1, 1, 7, 7, 7] 198 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37]) total number of confs: 918 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919720 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919720 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919720/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919720 Building REAL300004919721 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919721' /scratch/stefan/7775247/working/building/REAL300004919721 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919721 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919721/0 /scratch/stefan/7775247/working/building/REAL300004919721 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/726 `/scratch/stefan/7775247/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=CC=C1I)C(=O)[O-]) `REAL300004919721.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919721 none CC#CCC(NC(=O)CC1=CC=CC=C1I)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 18, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 92, 41, 41, 6, 41, 1, 1, 1, 1, 1, 1, 1, 1, 92, 137, 137, 201, 201, 201, 201, 201, 92, 41, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 999 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919721 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919721 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919721/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919721 Building REAL300004919722 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919722' /scratch/stefan/7775247/working/building/REAL300004919722 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919722 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919722/0 /scratch/stefan/7775247/working/building/REAL300004919722 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 727) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/727 `/scratch/stefan/7775247/working/3D/727' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1OC(F)(F)F)C(=O)[O-]) `REAL300004919722.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919722 none CC#CCC(NC(=O)C1=CC=CC=C1OC(F)(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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', 'F', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1] 2 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 7 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919722 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919722 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919722/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919722 Building REAL300004919723 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919723' /scratch/stefan/7775247/working/building/REAL300004919723 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919723 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919723/0 /scratch/stefan/7775247/working/building/REAL300004919723 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/728 `/scratch/stefan/7775247/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C2=CC=CC=C2)N(C)N=C1)C(=O)[O-]) `REAL300004919723.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919723 none CC#CCC(NC(=O)C1=C(C2=CC=CC=C2)N(C)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [127, 127, 127, 52, 13, 13, 1, 13, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 1, 1, 52, 81, 81, 127, 127, 127, 127, 127, 52, 13, 4, 4, 1, 4, 4, 2, 2, 2, 1] 154 rigid atoms, others: [38, 6, 8, 9, 10, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 629 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919723 none CC#CCC(NC(=O)C1=C(C2=CC=CC=C2)N(C)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 8, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [154, 154, 154, 87, 32, 32, 4, 32, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 87, 108, 108, 154, 154, 154, 154, 154, 87, 32, 1, 1, 1, 1, 1, 4, 4, 4, 4] 154 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38]) total number of confs: 691 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919723 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919723 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919723/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919723 Building REAL300004919724 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919724' /scratch/stefan/7775247/working/building/REAL300004919724 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919724 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919724/0 /scratch/stefan/7775247/working/building/REAL300004919724 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 729) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/729 `/scratch/stefan/7775247/working/3D/729' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CSC2=CC=C(Cl)C=C12)C(=O)[O-]) `REAL300004919724.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919724 none CC#CCC(NC(=O)CC1=CSC2=CC=C(Cl)C=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 14, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 94, 44, 44, 8, 44, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 94, 137, 137, 201, 201, 201, 201, 201, 94, 44, 8, 8, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 990 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919724 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919724 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919724/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919724 Building REAL300004919725 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919725' /scratch/stefan/7775247/working/building/REAL300004919725 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919725 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919725/0 /scratch/stefan/7775247/working/building/REAL300004919725 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/730 `/scratch/stefan/7775247/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CN=C1C(F)(F)F)C(=O)[O-]) `REAL300004919725.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919725 none CC#CCC(NC(=O)C1=CC=CN=C1C(F)(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 16, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 23, 23, 46, 46, 46, 46, 46, 16, 6, 1, 1, 1] 46 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919725 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919725 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919725/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919725 Building REAL300004919726 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919726' /scratch/stefan/7775247/working/building/REAL300004919726 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919726 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919726/0 /scratch/stefan/7775247/working/building/REAL300004919726 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 731) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/731 `/scratch/stefan/7775247/working/3D/731' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(C)=C1Br)C(=O)[O-]) `REAL300004919726.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919726 none CC#CCC(NC(=O)C1=CC=CC(C)=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 5, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 23, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 23, 35, 35, 60, 60, 60, 60, 60, 23, 7, 1, 1, 1, 2, 2, 2] 60 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 294 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919726 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919726 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919726/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919726 Building REAL300004919727 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919727' /scratch/stefan/7775247/working/building/REAL300004919727 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919727 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919727/0 /scratch/stefan/7775247/working/building/REAL300004919727 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/732 `/scratch/stefan/7775247/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C)C=C1Br)C(=O)[O-]) `REAL300004919727.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919727 none CC#CCC(NC(=O)C1=CC=C(C)C=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 22, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 22, 31, 31, 54, 54, 54, 54, 54, 22, 7, 1, 1, 2, 2, 2, 1] 54 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919727 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919727 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919727/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919727 Building REAL300004919728 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919728' /scratch/stefan/7775247/working/building/REAL300004919728 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919728 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919728/0 /scratch/stefan/7775247/working/building/REAL300004919728 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 733) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/733 `/scratch/stefan/7775247/working/3D/733' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(OC(F)(F)F)=C1)C(=O)[O-]) `REAL300004919728.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919728 none CC#CCC(NC(=O)C1=CC=CC(OC(F)(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 17, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 9, 16, 16, 16, 1, 17, 31, 31, 64, 64, 64, 64, 64, 17, 6, 1, 1, 1, 1] 176 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 336 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919728 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919728 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919728/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919728 Building REAL300004919729 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919729' /scratch/stefan/7775247/working/building/REAL300004919729 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919729 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919729/0 /scratch/stefan/7775247/working/building/REAL300004919729 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/734 `/scratch/stefan/7775247/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC2=CC=C(C(F)(F)F)C=N2)C=C1)C(=O)[O-]) `REAL300004919729.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919729 none CC#CCC(NC(=O)C1=CC=C(OC2=CC=C(C(F)(F)F)C=N2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 9, 13, 13, 25, 25, 25, 25, 25, 9, 3, 1, 1, 30, 30, 30, 1, 1] 201 rigid atoms, others: [35, 36, 6, 8, 9, 10, 11, 12, 40, 41, 23, 24] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919729 none CC#CCC(NC(=O)C1=CC=C(OC2=CC=C(C(F)(F)F)C=N2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 56, 56, 30, 56, 29, 30, 30, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 30, 30, 119, 154, 154, 201, 201, 201, 201, 201, 119, 56, 30, 30, 1, 1, 1, 30, 30] 201 rigid atoms, others: [37, 38, 39, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41]) total number of confs: 995 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919729 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919729 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919729/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919729 Building REAL300004919730 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919730' /scratch/stefan/7775247/working/building/REAL300004919730 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919730 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919730/0 /scratch/stefan/7775247/working/building/REAL300004919730 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 735) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/735 `/scratch/stefan/7775247/working/3D/735' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CN1C2=CC=CC=C2N=C1CS(C)(=O)=O)C(=O)[O-]) `REAL300004919730.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919730 none CC#CCC(NC(=O)CN1C2=CC=CC=C2N=C1CS(C)(=O)=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 14, 5, 11, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [141, 141, 141, 70, 30, 29, 5, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 13, 13, 13, 70, 97, 97, 141, 141, 141, 141, 141, 70, 29, 5, 5, 1, 1, 1, 1, 4, 4, 14, 14, 14] 201 rigid atoms, others: [35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 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: 729 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919730 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919730 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919730/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919730 Building REAL300004919731 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919731' /scratch/stefan/7775247/working/building/REAL300004919731 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919731 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919731/0 /scratch/stefan/7775247/working/building/REAL300004919731 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/736 `/scratch/stefan/7775247/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CC=CS2)N=C1C)C(=O)[O-]) `REAL300004919731.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919731 none CC#CCC(NC(=O)C1=CC=C(C2=CC=CS2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 14, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 36, 10, 10, 1, 10, 1, 1, 1, 1, 1, 12, 12, 12, 12, 1, 1, 1, 36, 59, 59, 101, 101, 101, 101, 101, 36, 10, 1, 1, 13, 12, 12, 2, 2, 2] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 505 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919731 none CC#CCC(NC(=O)C1=CC=C(C2=CC=CS2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 14, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 79, 79, 12, 79, 12, 12, 12, 1, 1, 1, 1, 1, 1, 12, 12, 13, 139, 168, 168, 201, 201, 201, 201, 201, 139, 79, 13, 13, 1, 1, 1, 13, 13, 13] 201 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 897 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919731 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919731 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919731/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919731 Building REAL300004919732 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919732' /scratch/stefan/7775247/working/building/REAL300004919732 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919732 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919732/0 /scratch/stefan/7775247/working/building/REAL300004919732 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 737) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/737 `/scratch/stefan/7775247/working/3D/737' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CC=CC=C2)N=C1C)C(=O)[O-]) `REAL300004919732.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919732 none CC#CCC(NC(=O)C1=CC=C(C2=CC=CC=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 35, 10, 10, 1, 10, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 1, 1, 1, 35, 53, 53, 101, 101, 101, 101, 101, 35, 10, 1, 1, 7, 7, 2, 7, 7, 2, 2, 2] 164 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 491 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919732 none CC#CCC(NC(=O)C1=CC=C(C2=CC=CC=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [164, 164, 164, 98, 45, 45, 7, 45, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 98, 121, 121, 164, 164, 164, 164, 164, 98, 45, 7, 7, 1, 1, 1, 1, 1, 7, 7, 7] 164 rigid atoms, others: [33, 34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40]) total number of confs: 755 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919732 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919732 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919732/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919732 Building REAL300004919733 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919733' /scratch/stefan/7775247/working/building/REAL300004919733 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919733 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919733/0 /scratch/stefan/7775247/working/building/REAL300004919733 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/738 `/scratch/stefan/7775247/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C(F)(F)F)N(C2=CC=CC(C)=C2)N=C1)C(=O)[O-]) `REAL300004919733.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919733 none CC#CCC(NC(=O)C1=C(C(F)(F)F)N(C2=CC=CC(C)=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 15, 15, 15, 8, 1, 1, 1, 1, 1, 5, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 9, 9, 1, 9, 1, 1, 1, 2, 2, 2, 1, 1, 7, 7, 3, 7, 7, 7, 1, 1, 27, 42, 42, 64, 64, 64, 64, 64, 27, 9, 7, 7, 7, 7, 7, 7, 7, 1] 201 rigid atoms, others: [6, 8, 9, 10, 14, 15, 41, 22, 23] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 352 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919733 none CC#CCC(NC(=O)C1=C(C(F)(F)F)N(C2=CC=CC(C)=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 15, 15, 15, 8, 1, 1, 1, 1, 1, 5, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 111, 41, 41, 7, 41, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 111, 143, 143, 201, 201, 201, 201, 201, 111, 41, 1, 1, 1, 2, 2, 2, 1, 7] 201 rigid atoms, others: [34, 35, 36, 40, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 41]) total number of confs: 951 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919733 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919733 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919733/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919733 Building REAL300004919734 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919734' /scratch/stefan/7775247/working/building/REAL300004919734 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919734 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919734/0 /scratch/stefan/7775247/working/building/REAL300004919734 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 739) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/739 `/scratch/stefan/7775247/working/3D/739' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N=C2C(=C1)C=NN2C(C)C)C(=O)[O-]) `REAL300004919734.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919734 none CC#CCC(NC(=O)C1=C(C)N=C2C(=C1)C=NN2C(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 8, 8, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [138, 138, 138, 40, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 40, 66, 66, 138, 138, 138, 138, 138, 40, 10, 2, 2, 2, 1, 1, 12, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 670 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919734 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919734 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919734/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919734 Building REAL300004919735 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919735' /scratch/stefan/7775247/working/building/REAL300004919735 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919735 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919735/0 /scratch/stefan/7775247/working/building/REAL300004919735 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/740 `/scratch/stefan/7775247/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C2CCC3=C2C1=CC=C3)C(=O)[O-]) `REAL300004919735.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919735 none CC#CCC(NC(=O)C1=CC=C2CCC3=C2C1=CC=C3)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 34, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 49, 49, 81, 81, 81, 81, 81, 34, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1] 81 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 380 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919735 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919735 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919735/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919735 Building REAL300004919736 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919736' /scratch/stefan/7775247/working/building/REAL300004919736 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919736 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919736/0 /scratch/stefan/7775247/working/building/REAL300004919736 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 741) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/741 `/scratch/stefan/7775247/working/3D/741' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=CC=C(OC)C=C2N=C1C)C(=O)[O-]) `REAL300004919736.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919736 none CC#CCC(NC(=O)C1=CC2=CC=C(OC)C=C2N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 8, 1, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 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: [93, 93, 93, 40, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 40, 61, 61, 93, 93, 93, 93, 93, 40, 10, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2] 124 rigid atoms, others: [32, 33, 37, 6, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 38, 39, 40]) total number of confs: 452 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919736 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919736 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919736/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919736 Building REAL300004919737 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919737' /scratch/stefan/7775247/working/building/REAL300004919737 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919737 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919737/0 /scratch/stefan/7775247/working/building/REAL300004919737 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/742 `/scratch/stefan/7775247/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(CC2=CC=CC=C2Cl)C(=O)C=C1)C(=O)[O-]) `REAL300004919737.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919737 none CC#CCC(NC(=O)C1=CN(CC2=CC=CC=C2Cl)C(=O)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 16, 1, 11, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 5, 5, 1, 5, 1, 1, 1, 1, 5, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 13, 18, 18, 28, 28, 28, 28, 28, 13, 5, 1, 5, 5, 13, 13, 13, 13, 1, 1] 201 rigid atoms, others: [33, 6, 8, 9, 10, 11, 40, 19, 20, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919737 none CC#CCC(NC(=O)C1=CN(CC2=CC=CC=C2Cl)C(=O)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 16, 1, 11, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 107, 46, 46, 13, 46, 13, 13, 6, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 107, 149, 149, 201, 201, 201, 201, 201, 107, 46, 13, 6, 6, 1, 1, 1, 1, 13, 13] 201 rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41]) total number of confs: 1024 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919737 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919737 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919737/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919737 Building REAL300004919738 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919738' /scratch/stefan/7775247/working/building/REAL300004919738 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919738 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919738/0 /scratch/stefan/7775247/working/building/REAL300004919738 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 743) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/743 `/scratch/stefan/7775247/working/3D/743' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C2C(C)=NOC2=NC(C(C)C)=C1)C(=O)[O-]) `REAL300004919738.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919738 none CC#CCC(NC(=O)C1=C2C(C)=NOC2=NC(C(C)C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 5, 8, 12, 1, 8, 1, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 35, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 35, 54, 54, 88, 88, 88, 88, 88, 35, 9, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 1] 143 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 41] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 440 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919738 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919738 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919738/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919738 Building REAL300004919739 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919739' /scratch/stefan/7775247/working/building/REAL300004919739 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919739 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919739/0 /scratch/stefan/7775247/working/building/REAL300004919739 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/744 `/scratch/stefan/7775247/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C2C=NN(C(C)C)C2=NC(C)=C1)C(=O)[O-]) `REAL300004919739.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919739 none CC#CCC(NC(=O)C1=C2C=NN(C(C)C)C2=NC(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 8, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [130, 130, 130, 43, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 12, 12, 1, 1, 1, 1, 1, 43, 73, 73, 130, 130, 130, 130, 130, 43, 11, 1, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 1] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 42, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 668 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919739 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919739 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919739/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919739 Building REAL300004919740 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919740' /scratch/stefan/7775247/working/building/REAL300004919740 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919740 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919740/0 /scratch/stefan/7775247/working/building/REAL300004919740 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 745) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/745 `/scratch/stefan/7775247/working/3D/745' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C2C(C)=NOC2=NC(C2=CC=CO2)=C1)C(=O)[O-]) `REAL300004919740.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919740 none CC#CCC(NC(=O)C1=C2C(C)=NOC2=NC(C2=CC=CO2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 5, 8, 12, 1, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 34, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 1, 34, 54, 54, 96, 96, 96, 96, 96, 34, 10, 2, 2, 2, 12, 12, 12, 1] 201 rigid atoms, others: [6, 39, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 467 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919740 none CC#CCC(NC(=O)C1=C2C(C)=NOC2=NC(C2=CC=CO2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 5, 8, 12, 1, 8, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 70, 70, 13, 70, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 12, 133, 154, 154, 201, 201, 201, 201, 201, 133, 70, 13, 13, 13, 1, 1, 1, 12] 201 rigid atoms, others: [36, 37, 38, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39]) total number of confs: 907 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919740 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919740 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919740/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919740 Building REAL300004919741 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919741' /scratch/stefan/7775247/working/building/REAL300004919741 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919741 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919741/0 /scratch/stefan/7775247/working/building/REAL300004919741 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/746 `/scratch/stefan/7775247/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C2C(C)=NOC2=NC(C2=C(C)OC(C)=C2)=C1)C(=O)[O-]) `REAL300004919741.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919741 none CC#CCC(NC(=O)C1=C2C(C)=NOC2=NC(C2=C(C)OC(C)=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 5, 8, 12, 1, 8, 1, 1, 1, 5, 12, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 27, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 1, 27, 40, 40, 61, 61, 61, 61, 61, 27, 9, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 1] 201 rigid atoms, others: [45, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 321 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919741 none CC#CCC(NC(=O)C1=C2C(C)=NOC2=NC(C2=C(C)OC(C)=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 5, 8, 12, 1, 8, 1, 1, 1, 5, 12, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 120, 59, 59, 10, 59, 10, 9, 9, 9, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 10, 120, 154, 154, 201, 201, 201, 201, 201, 120, 59, 10, 10, 10, 2, 2, 2, 2, 2, 2, 1, 10] 201 rigid atoms, others: [44, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45]) total number of confs: 974 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919741 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919741 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919741/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919741 Building REAL300004919742 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919742' /scratch/stefan/7775247/working/building/REAL300004919742 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919742 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919742/0 /scratch/stefan/7775247/working/building/REAL300004919742 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 747) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/747 `/scratch/stefan/7775247/working/3D/747' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C2C=NN(C(C)C)C2=NC(C2=CC=CS2)=C1)C(=O)[O-]) `REAL300004919742.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919742 none CC#CCC(NC(=O)C1=C2C=NN(C(C)C)C2=NC(C2=CC=CS2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 14, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 6, 6, 1, 1, 1, 1, 12, 12, 12, 12, 1, 26, 41, 41, 64, 64, 64, 64, 64, 26, 11, 1, 6, 7, 7, 7, 7, 7, 7, 12, 12, 12, 1] 201 rigid atoms, others: [35, 6, 8, 9, 10, 11, 12, 13, 46, 16, 17, 18, 19, 24] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 356 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919742 none CC#CCC(NC(=O)C1=C2C=NN(C(C)C)C2=NC(C2=CC=CS2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 14, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [176, 176, 176, 113, 62, 62, 12, 62, 12, 12, 12, 12, 12, 12, 47, 47, 12, 12, 1, 1, 1, 1, 1, 1, 12, 113, 149, 149, 176, 176, 176, 176, 176, 113, 62, 12, 46, 47, 47, 47, 47, 47, 47, 1, 1, 1, 12] 201 rigid atoms, others: [43, 44, 45, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 46]) total number of confs: 973 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919742 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919742 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919742/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919742 Building REAL300004919743 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919743' /scratch/stefan/7775247/working/building/REAL300004919743 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919743 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919743/0 /scratch/stefan/7775247/working/building/REAL300004919743 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/748 `/scratch/stefan/7775247/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=C(C)N2N=C3C=CC=CC3=C2N=C1C)C(=O)[O-]) `REAL300004919743.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919743 none CC#CCC(NC(=O)CCC1=C(C)N2N=C3C=CC=CC3=C2N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [74, 74, 74, 52, 19, 19, 3, 19, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 61, 61, 74, 74, 74, 74, 74, 53, 19, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2] 74 rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48]) total number of confs: 368 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919743 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919743 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919743/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919743 Building REAL300004919744 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919744' /scratch/stefan/7775247/working/building/REAL300004919744 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919744 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919744/0 /scratch/stefan/7775247/working/building/REAL300004919744 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 749) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/749 `/scratch/stefan/7775247/working/3D/749' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C2C(C)=NOC2=NC(C2=CC=C(F)C=C2)=C1)C(=O)[O-]) `REAL300004919744.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919744 none CC#CCC(NC(=O)C1=C2C(C)=NOC2=NC(C2=CC=C(F)C=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 5, 8, 12, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 98, 36, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 1, 1, 6, 6, 1, 36, 52, 52, 98, 98, 98, 98, 98, 36, 10, 2, 2, 2, 6, 6, 6, 6, 1] 168 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 42] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 467 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919744 none CC#CCC(NC(=O)C1=C2C(C)=NOC2=NC(C2=CC=C(F)C=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 5, 8, 12, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [168, 168, 168, 119, 44, 44, 6, 44, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 119, 137, 137, 168, 168, 168, 168, 168, 119, 44, 7, 7, 7, 1, 1, 1, 1, 6] 168 rigid atoms, others: [38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42]) total number of confs: 761 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919744 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919744 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919744/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919744 Building REAL300004919745 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919745' /scratch/stefan/7775247/working/building/REAL300004919745 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919745 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919745/0 /scratch/stefan/7775247/working/building/REAL300004919745 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/750 `/scratch/stefan/7775247/working/3D/750' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NC2=CC=C(OC)C=C2C=C1)C(=O)[O-]) `REAL300004919745.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919745 none CC#CCC(NC(=O)C1=NC2=CC=C(OC)C=C2C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 32, 13, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 32, 48, 48, 75, 75, 75, 75, 75, 32, 13, 1, 1, 2, 2, 2, 1, 1, 1] 95 rigid atoms, others: [35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 32, 34, 15, 33, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 359 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919745 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919745 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919745/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919745 Building REAL300004919746 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919746' /scratch/stefan/7775247/working/building/REAL300004919746 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919746 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919746/0 /scratch/stefan/7775247/working/building/REAL300004919746 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 751) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/751 `/scratch/stefan/7775247/working/3D/751' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C2C=NN(CC)C2=NC(C2=CC=CC=C2)=C1)C(=O)[O-]) `REAL300004919746.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919746 none CC#CCC(NC(=O)C1=C2C=NN(CC)C2=NC(C2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 24, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 6, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 24, 39, 39, 60, 60, 60, 60, 60, 24, 10, 1, 6, 6, 6, 6, 6, 6, 6, 1, 6, 6, 1] 201 rigid atoms, others: [35, 6, 8, 9, 10, 11, 12, 13, 46, 15, 16, 17, 18, 24] set([0, 1, 2, 3, 4, 5, 7, 14, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 340 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919746 none CC#CCC(NC(=O)C1=C2C=NN(CC)C2=NC(C2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [190, 190, 190, 87, 43, 43, 6, 43, 6, 6, 6, 6, 6, 6, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 87, 132, 132, 190, 190, 190, 190, 190, 87, 43, 6, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 6] 201 rigid atoms, others: [41, 42, 43, 44, 45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46]) total number of confs: 1021 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919746 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919746 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919746/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919746 Building REAL300004919747 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919747' /scratch/stefan/7775247/working/building/REAL300004919747 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919747 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919747/0 /scratch/stefan/7775247/working/building/REAL300004919747 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/752 `/scratch/stefan/7775247/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NOC(C2=CC=C(Cl)C=C2)=C1)C(=O)[O-]) `REAL300004919747.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919747 none CC#CCC(NC(=O)C1=NOC(C2=CC=C(Cl)C=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 39, 12, 12, 1, 12, 1, 1, 1, 1, 1, 6, 6, 1, 4, 6, 6, 1, 39, 63, 63, 114, 114, 114, 114, 114, 39, 12, 7, 7, 7, 7, 1] 150 rigid atoms, others: [34, 6, 8, 9, 10, 11, 12, 19] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 563 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919747 none CC#CCC(NC(=O)C1=NOC(C2=CC=C(Cl)C=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [150, 150, 150, 103, 51, 51, 6, 52, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 103, 123, 123, 150, 150, 150, 150, 150, 103, 51, 1, 1, 1, 1, 7] 150 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 681 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919747 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919747 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919747/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919747 Building REAL300004919748 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919748' /scratch/stefan/7775247/working/building/REAL300004919748 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919748 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919748/0 /scratch/stefan/7775247/working/building/REAL300004919748 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 753) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/753 `/scratch/stefan/7775247/working/3D/753' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C2C(C)=NN(C)C2=NC(C2=CC=CC=C2)=C1)C(=O)[O-]) `REAL300004919748.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919748 none CC#CCC(NC(=O)C1=C2C(C)=NN(C)C2=NC(C2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 5, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [81, 81, 81, 30, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 30, 44, 44, 81, 81, 81, 81, 81, 30, 8, 2, 2, 2, 2, 2, 2, 6, 6, 1, 6, 6, 1] 146 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 46] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 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: 398 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: REAL300004919748 none CC#CCC(NC(=O)C1=C2C(C)=NN(C)C2=NC(C2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 5, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 146, 93, 36, 36, 6, 36, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 93, 118, 118, 146, 146, 146, 146, 146, 93, 36, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 6] 146 rigid atoms, others: [41, 42, 43, 44, 45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46]) total number of confs: 716 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919748 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919748 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919748/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919748 Building REAL300004919749 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919749' /scratch/stefan/7775247/working/building/REAL300004919749 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919749 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919749/0 /scratch/stefan/7775247/working/building/REAL300004919749 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/754 `/scratch/stefan/7775247/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CN1C2=CC=CC=C2C(=O)C2=CC=CC=C21)C(=O)[O-]) `REAL300004919749.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919749 none CC#CCC(NC(=O)CN1C2=CC=CC=C2C(=O)C2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 97, 52, 21, 20, 4, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 73, 73, 97, 97, 97, 97, 97, 52, 20, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1] 97 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 34, 33, 35, 32, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 494 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919749 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919749 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919749/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919749 Building REAL300004919750 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919750' /scratch/stefan/7775247/working/building/REAL300004919750 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919750 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919750/0 /scratch/stefan/7775247/working/building/REAL300004919750 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 755) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/755 `/scratch/stefan/7775247/working/3D/755' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C2C(C)=NN(C)C2=NC(C2=CC=CS2)=C1)C(=O)[O-]) `REAL300004919750.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919750 none CC#CCC(NC(=O)C1=C2C(C)=NN(C)C2=NC(C2=CC=CS2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 5, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 14, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 29, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 1, 29, 45, 45, 76, 76, 76, 76, 76, 29, 9, 2, 2, 2, 2, 2, 2, 12, 12, 12, 1] 201 rigid atoms, others: [43, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 389 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919750 none CC#CCC(NC(=O)C1=C2C(C)=NN(C)C2=NC(C2=CC=CS2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 5, 8, 8, 5, 1, 8, 1, 1, 1, 1, 1, 14, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 66, 66, 12, 66, 12, 12, 12, 12, 12, 12, 13, 12, 12, 1, 1, 1, 1, 1, 1, 12, 131, 157, 157, 201, 201, 201, 201, 201, 131, 66, 13, 13, 13, 13, 13, 13, 1, 1, 1, 12] 201 rigid atoms, others: [40, 41, 42, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43]) total number of confs: 927 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919750 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919750 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919750/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919750 Building REAL300004919751 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919751' /scratch/stefan/7775247/working/building/REAL300004919751 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919751 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919751/0 /scratch/stefan/7775247/working/building/REAL300004919751 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/756 `/scratch/stefan/7775247/working/3D/756' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CSC(CC2=CC=CC=C2F)C(=O)N1)C(=O)[O-]) `REAL300004919751.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919751 none CC#CCC(NC(=O)C1CSC(CC2=CC=CC=C2F)C(=O)N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'N.am', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 5, 14, 5, 5, 1, 1, 1, 1, 1, 1, 15, 1, 11, 8, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 26, 10, 10, 1, 10, 1, 1, 1, 1, 1, 4, 13, 13, 4, 13, 13, 13, 1, 1, 1, 26, 44, 44, 67, 67, 67, 67, 67, 26, 10, 1, 1, 1, 1, 4, 4, 13, 13, 8, 13, 1] 201 rigid atoms, others: [33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 43, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 382 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919751 none CC#CCC(NC(=O)C1CSC(CC2=CC=CC=C2F)C(=O)N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'N.am', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 5, 14, 5, 5, 1, 1, 1, 1, 1, 1, 15, 1, 11, 8, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 113, 56, 56, 13, 56, 13, 13, 13, 7, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 113, 151, 151, 201, 201, 201, 201, 201, 113, 56, 13, 13, 13, 13, 7, 7, 1, 1, 1, 1, 13] 201 rigid atoms, others: [39, 40, 41, 42, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43]) total number of confs: 999 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919751 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919751 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919751/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919751 Building REAL300004919752 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919752' /scratch/stefan/7775247/working/building/REAL300004919752 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919752 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919752/0 /scratch/stefan/7775247/working/building/REAL300004919752 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 757) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/757 `/scratch/stefan/7775247/working/3D/757' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=CC(F)=C2)C(C2=CC=CS2)=N1)C(=O)[O-]) `REAL300004919752.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919752 none CC#CCC(NC(=O)C1=NN(C2=CC=CC(F)=C2)C(C2=CC=CS2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 14, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 6, 1, 6, 1, 1, 1, 1, 9, 9, 7, 9, 9, 9, 1, 1, 7, 7, 7, 7, 1, 18, 25, 25, 34, 34, 34, 34, 34, 18, 6, 9, 9, 9, 9, 7, 7, 7] 201 rigid atoms, others: [6, 8, 9, 10, 11, 18, 19, 24] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) 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: REAL300004919752 none CC#CCC(NC(=O)C1=NN(C2=CC=CC(F)=C2)C(C2=CC=CS2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 14, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 110, 65, 30, 30, 7, 30, 7, 7, 7, 7, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 7, 65, 82, 82, 110, 110, 110, 110, 110, 65, 30, 16, 16, 16, 16, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) 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: REAL300004919752 none CC#CCC(NC(=O)C1=NN(C2=CC=CC(F)=C2)C(C2=CC=CS2)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 14, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [126, 126, 126, 81, 38, 38, 9, 38, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 16, 16, 16, 16, 9, 81, 97, 97, 126, 126, 126, 126, 126, 81, 38, 1, 1, 1, 1, 16, 16, 16] 201 rigid atoms, others: [35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41]) total number of confs: 570 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919752 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919752 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919752/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919752 Building REAL300004919753 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919753' /scratch/stefan/7775247/working/building/REAL300004919753 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919753 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919753/0 /scratch/stefan/7775247/working/building/REAL300004919753 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/758 `/scratch/stefan/7775247/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=C(C=CC3=C2C=CC=C3)N1)C(=O)[O-]) `REAL300004919753.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919753 none CC#CCC(NC(=O)C1=CC2=C(C=CC3=C2C=CC=C3)N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 40, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 51, 51, 70, 70, 70, 70, 70, 40, 13, 1, 1, 1, 1, 1, 1, 1, 1] 70 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 7, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 332 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919753 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919753 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919753/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919753 Building REAL300004919754 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919754' /scratch/stefan/7775247/working/building/REAL300004919754 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919754 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919754/0 /scratch/stefan/7775247/working/building/REAL300004919754 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 759) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/759 `/scratch/stefan/7775247/working/3D/759' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(OC)C=CC(SC)=C1OC)C(=O)[O-]) `REAL300004919754.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919754 none CC#CCC(NC(=O)C1=C(OC)C=CC(SC)=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 12, 5, 1, 1, 1, 14, 5, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 28, 12, 12, 1, 12, 1, 1, 1, 3, 1, 1, 1, 1, 9, 1, 1, 2, 28, 42, 42, 74, 74, 74, 74, 74, 28, 12, 4, 4, 4, 1, 1, 9, 9, 9, 2, 2, 2] 201 rigid atoms, others: [33, 34, 6, 8, 9, 10, 12, 13, 14, 15, 17, 18] set([0, 1, 2, 3, 4, 5, 7, 11, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 362 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919754 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919754 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919754/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919754 Building REAL300004919755 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919755' /scratch/stefan/7775247/working/building/REAL300004919755 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919755 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919755/0 /scratch/stefan/7775247/working/building/REAL300004919755 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/760 `/scratch/stefan/7775247/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=CC(S(=O)(=O)CC)=C1)C(=O)[O-]) `REAL300004919755.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919755 none CC#CCC(NC(=O)CC1=CC=CC(S(=O)(=O)CC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 1, 14, 11, 11, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [121, 121, 121, 46, 16, 16, 6, 16, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 12, 1, 46, 67, 67, 121, 121, 121, 121, 121, 46, 16, 6, 6, 1, 1, 1, 12, 12, 12, 12, 12, 1] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 40, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39]) total number of confs: 616 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919755 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919755 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919755/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919755 Building REAL300004919756 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919756' /scratch/stefan/7775247/working/building/REAL300004919756 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919756 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919756/0 /scratch/stefan/7775247/working/building/REAL300004919756 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 761) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/761 `/scratch/stefan/7775247/working/3D/761' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)C1=C(C)N(CC(F)(F)F)N=C1C)C(=O)[O-]) `REAL300004919756.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919756 none CC#CCC(NC(=O)C(C)C1=C(C)N(CC(F)(F)F)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 5, 1, 1, 5, 8, 5, 5, 15, 15, 15, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 46, 18, 18, 5, 18, 1, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 46, 67, 67, 100, 100, 100, 100, 100, 46, 18, 5, 5, 5, 5, 2, 2, 2, 5, 5, 2, 2, 2] 201 rigid atoms, others: [8, 10, 11, 12, 13, 14, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 530 number of broken/clashed sets: 175 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919756 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919756 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919756/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919756 Building REAL300004919757 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919757' /scratch/stefan/7775247/working/building/REAL300004919757 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919757 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919757/0 /scratch/stefan/7775247/working/building/REAL300004919757 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/762 `/scratch/stefan/7775247/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C)=CC(C)=C1Br)C(=O)[O-]) `REAL300004919757.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919757 none CC#CCC(NC(=O)C1=CC(C)=CC(C)=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 5, 1, 1, 5, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 34, 34, 60, 60, 60, 60, 60, 25, 7, 1, 2, 2, 2, 1, 2, 2, 2] 60 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 31] set([0, 1, 2, 3, 4, 5, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34]) total number of confs: 279 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919757 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919757 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919757/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919757 Building REAL300004919758 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919758' /scratch/stefan/7775247/working/building/REAL300004919758 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919758 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919758/0 /scratch/stefan/7775247/working/building/REAL300004919758 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 763) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/763 `/scratch/stefan/7775247/working/3D/763' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(F)=CC2=C1NC1=CC=C(F)C=C1C2=O)C(=O)[O-]) `REAL300004919758.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919758 none CC#CCC(NC(=O)C1=CC(F)=CC2=C1NC1=CC=C(F)C=C1C2=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 15, 1, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 36, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 48, 48, 66, 66, 66, 66, 66, 36, 11, 1, 1, 1, 1, 1, 1] 66 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 7, 34, 33, 32, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 320 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919758 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919758 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919758/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919758 Building REAL300004919759 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919759' /scratch/stefan/7775247/working/building/REAL300004919759 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919759 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919759/0 /scratch/stefan/7775247/working/building/REAL300004919759 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/764 `/scratch/stefan/7775247/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCN1C(=O)C1=CC=C(Cl)C(Cl)=C1)C(=O)[O-]) `REAL300004919759.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919759 none CC#CCC(NC(=O)C1CCCN1C(=O)C1=CC=C(Cl)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [42, 42, 42, 20, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 12, 17, 17, 17, 17, 20, 30, 30, 42, 42, 42, 42, 42, 20, 8, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17] 121 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42]) total number of confs: 255 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919759 none CC#CCC(NC(=O)C1CCCN1C(=O)C1=CC=C(Cl)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 16, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [121, 121, 121, 73, 40, 40, 17, 40, 17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 73, 99, 99, 121, 121, 121, 121, 121, 73, 40, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1] 121 rigid atoms, others: [40, 41, 42, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 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: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919759 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919759 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919759/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919759 Building REAL300004919760 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919760' /scratch/stefan/7775247/working/building/REAL300004919760 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919760 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919760/0 /scratch/stefan/7775247/working/building/REAL300004919760 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 765) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/765 `/scratch/stefan/7775247/working/3D/765' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C)=NC2=CC=C(Br)C=C21)C(=O)[O-]) `REAL300004919760.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919760 none CC#CCC(NC(=O)C1=CC(C)=NC2=CC=C(Br)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 5, 8, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 37, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 53, 53, 86, 86, 86, 86, 86, 37, 9, 1, 2, 2, 2, 1, 1, 1] 86 rigid atoms, others: [34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 32, 33, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31]) total number of confs: 398 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919760 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919760 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919760/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919760 Building REAL300004919761 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919761' /scratch/stefan/7775247/working/building/REAL300004919761 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919761 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919761/0 /scratch/stefan/7775247/working/building/REAL300004919761 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/766 `/scratch/stefan/7775247/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(NC(=O)C2=CC=CN=C2)=C1)C(=O)[O-]) `REAL300004919761.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919761 none CC#CCC(NC(=O)C1=CC=CC(NC(=O)C2=CC=CN=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 15, 15, 15, 15, 1, 17, 29, 29, 59, 59, 59, 59, 59, 17, 5, 1, 1, 1, 7, 15, 15, 15, 15, 1] 201 rigid atoms, others: [33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 22, 41] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40]) total number of confs: 298 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919761 none CC#CCC(NC(=O)C1=CC=CC(NC(=O)C2=CC=CN=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 108, 43, 43, 15, 43, 15, 15, 15, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 15, 108, 146, 146, 201, 201, 201, 201, 201, 108, 43, 15, 15, 15, 5, 1, 1, 1, 1, 15] 201 rigid atoms, others: [37, 38, 39, 40, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41]) total number of confs: 967 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919761 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919761 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919761/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919761 Building REAL300004919762 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919762' /scratch/stefan/7775247/working/building/REAL300004919762 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919762 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919762/0 /scratch/stefan/7775247/working/building/REAL300004919762 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 767) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/767 `/scratch/stefan/7775247/working/3D/767' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C2C(=NC(C3CC3)=C1)ON=C2C(C)C)C(=O)[O-]) `REAL300004919762.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919762 none CC#CCC(NC(=O)C1=C2C(=NC(C3CC3)=C1)ON=C2C(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 8, 1, 5, 5, 5, 1, 12, 8, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 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: [77, 77, 77, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 12, 12, 1, 1, 1, 1, 1, 2, 2, 25, 38, 38, 77, 77, 77, 77, 77, 25, 7, 12, 12, 12, 12, 12, 1, 2, 2, 2, 2, 2, 2, 2] 139 rigid atoms, others: [38, 6, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 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: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919762 none CC#CCC(NC(=O)C1=C2C(=NC(C3CC3)=C1)ON=C2C(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 8, 1, 5, 5, 5, 1, 12, 8, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 139, 92, 45, 45, 12, 45, 12, 12, 12, 12, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 92, 114, 114, 139, 139, 139, 139, 139, 92, 45, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12] 139 rigid atoms, others: [33, 34, 35, 36, 37, 12, 13, 14, 15] 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, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 628 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919762 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919762 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919762/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919762 Building REAL300004919763 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919763' /scratch/stefan/7775247/working/building/REAL300004919763 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919763 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919763/0 /scratch/stefan/7775247/working/building/REAL300004919763 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/768 `/scratch/stefan/7775247/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C2C(CC(C)(C)C)=NOC2=NC(C2CC2)=C1)C(=O)[O-]) `REAL300004919763.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919763 none CC#CCC(NC(=O)C1=C2C(CC(C)(C)C)=NOC2=NC(C2CC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 5, 5, 5, 5, 5, 8, 12, 1, 8, 1, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 24, 9, 9, 1, 9, 1, 1, 1, 1, 5, 6, 6, 6, 1, 1, 1, 1, 1, 1, 11, 11, 1, 24, 39, 39, 74, 74, 74, 74, 74, 24, 9, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 1] 201 rigid atoms, others: [51, 6, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 22, 23, 25, 26, 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: 398 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919763 none CC#CCC(NC(=O)C1=C2C(CC(C)(C)C)=NOC2=NC(C2CC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 5, 5, 5, 5, 5, 8, 12, 1, 8, 1, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [150, 150, 150, 92, 45, 45, 11, 45, 11, 11, 11, 11, 33, 37, 37, 37, 11, 11, 11, 11, 1, 1, 1, 1, 11, 92, 122, 122, 150, 150, 150, 150, 150, 92, 45, 33, 33, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 11] 201 rigid atoms, others: [46, 47, 48, 49, 50, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 51]) total number of confs: 832 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919763 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919763 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919763/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919763 Building REAL300004919764 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919764' /scratch/stefan/7775247/working/building/REAL300004919764 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919764 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919764/0 /scratch/stefan/7775247/working/building/REAL300004919764 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 769) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/769 `/scratch/stefan/7775247/working/3D/769' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(N2N=C(C)C=C2C)N=C1)C(=O)[O-]) `REAL300004919764.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919764 none CC#CCC(NC(=O)C1=CC=C(N2N=C(C)C=C2C)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 1, 1, 5, 8, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 25, 37, 37, 58, 58, 58, 58, 58, 25, 7, 1, 1, 4, 4, 4, 4, 4, 4, 4, 1] 70 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 40, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 280 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919764 none CC#CCC(NC(=O)C1=CC=C(N2N=C(C)C=C2C)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 1, 1, 5, 8, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 34, 11, 11, 4, 11, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 34, 44, 44, 70, 70, 70, 70, 70, 34, 11, 4, 4, 2, 2, 2, 1, 2, 2, 2, 4] 70 rigid atoms, others: [36, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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: 335 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919764 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919764 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919764/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919764 Building REAL300004919765 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919765' /scratch/stefan/7775247/working/building/REAL300004919765 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919765 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919765/0 /scratch/stefan/7775247/working/building/REAL300004919765 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/770 `/scratch/stefan/7775247/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OCC2=CC=CC=C2)N=C1)C(=O)[O-]) `REAL300004919765.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919765 none CC#CCC(NC(=O)C1=CC=C(OCC2=CC=CC=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 5, 21, 37, 37, 28, 37, 37, 1, 1, 14, 22, 22, 40, 40, 40, 40, 40, 14, 5, 1, 1, 21, 21, 37, 37, 37, 37, 37, 1] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 20, 21, 41] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 317 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919765 none CC#CCC(NC(=O)C1=CC=C(OCC2=CC=CC=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 125, 84, 84, 37, 84, 37, 37, 37, 16, 3, 1, 1, 1, 1, 1, 1, 1, 37, 37, 125, 153, 153, 201, 201, 201, 201, 201, 125, 84, 37, 37, 3, 3, 1, 1, 1, 1, 1, 37] 201 rigid atoms, others: [36, 37, 38, 39, 40, 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, 41]) total number of confs: 899 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919765 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919765 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919765/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919765 Building REAL300004919766 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919766' /scratch/stefan/7775247/working/building/REAL300004919766 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919766 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919766/0 /scratch/stefan/7775247/working/building/REAL300004919766 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 771) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/771 `/scratch/stefan/7775247/working/3D/771' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CN=C1OCC(F)(F)F)C(=O)[O-]) `REAL300004919766.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919766 none CC#CCC(NC(=O)C1=CC=CN=C1OCC(F)(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 12, 5, 5, 15, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 29, 29, 29, 29, 26, 43, 43, 64, 64, 64, 64, 64, 26, 11, 1, 1, 1, 29, 29] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 411 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919766 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919766 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919766/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919766 Building REAL300004919767 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919767' /scratch/stefan/7775247/working/building/REAL300004919767 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919767 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919767/0 /scratch/stefan/7775247/working/building/REAL300004919767 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/772 `/scratch/stefan/7775247/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC2=CC=CC=C2)N=C1)C(=O)[O-]) `REAL300004919767.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919767 none CC#CCC(NC(=O)C1=CC=C(OC2=CC=CC=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 8, 17, 17, 9, 17, 17, 1, 1, 15, 23, 23, 43, 43, 43, 43, 43, 15, 5, 1, 1, 17, 17, 10, 17, 17, 1] 201 rigid atoms, others: [32, 38, 6, 8, 9, 10, 11, 12, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) 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: REAL300004919767 none CC#CCC(NC(=O)C1=CC=C(OC2=CC=CC=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 107, 50, 50, 17, 50, 17, 17, 17, 5, 1, 1, 1, 1, 1, 1, 1, 17, 17, 107, 136, 136, 201, 201, 201, 201, 201, 107, 50, 17, 17, 1, 1, 1, 1, 1, 17] 201 rigid atoms, others: [33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38]) total number of confs: 915 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919767 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919767 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919767/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919767 Building REAL300004919768 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919768' /scratch/stefan/7775247/working/building/REAL300004919768 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919768 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919768/0 /scratch/stefan/7775247/working/building/REAL300004919768 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 773) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/773 `/scratch/stefan/7775247/working/3D/773' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COC1=CC=CC=C1Br)C(=O)[O-]) `REAL300004919768.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919768 none CC#CCC(NC(=O)COC1=CC=CC=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 134, 92, 92, 26, 92, 7, 1, 1, 1, 1, 1, 1, 1, 1, 134, 174, 174, 201, 201, 201, 201, 201, 134, 92, 26, 26, 1, 1, 1, 1] 201 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 1009 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919768 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919768 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919768/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919768 Building REAL300004919769 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919769' /scratch/stefan/7775247/working/building/REAL300004919769 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919769 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919769/0 /scratch/stefan/7775247/working/building/REAL300004919769 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/774 `/scratch/stefan/7775247/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=C(C=CC=C2)C2=C1N=CC=C2)C(=O)[O-]) `REAL300004919769.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919769 none CC#CCC(NC(=O)C1=CC2=C(C=CC=C2)C2=C1N=CC=C2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 31, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 43, 43, 68, 68, 68, 68, 68, 31, 12, 1, 1, 1, 1, 1, 1, 1, 1] 68 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 7, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 325 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919769 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919769 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919769/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919769 Building REAL300004919770 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919770' /scratch/stefan/7775247/working/building/REAL300004919770 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919770 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919770/0 /scratch/stefan/7775247/working/building/REAL300004919770 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 775) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/775 `/scratch/stefan/7775247/working/3D/775' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(Cl)C2=CC=CN=C12)C(=O)[O-]) `REAL300004919770.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919770 none CC#CCC(NC(=O)C1=CC=C(Cl)C2=CC=CN=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 33, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 51, 51, 76, 76, 76, 76, 76, 33, 12, 1, 1, 1, 1, 1] 76 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 385 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919770 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919770 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919770/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919770 Building REAL300004919771 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919771' /scratch/stefan/7775247/working/building/REAL300004919771 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919771 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919771/0 /scratch/stefan/7775247/working/building/REAL300004919771 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/776 `/scratch/stefan/7775247/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(N(C)C2=CC=CC=C2)N=C1)C(=O)[O-]) `REAL300004919771.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919771 none CC#CCC(NC(=O)C1=CC=C(N(C)C2=CC=CC=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 13, 13, 29, 29, 21, 29, 29, 1, 1, 17, 29, 29, 55, 55, 55, 55, 55, 17, 5, 1, 1, 13, 13, 13, 29, 29, 21, 29, 29, 1] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 20, 21, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 337 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919771 none CC#CCC(NC(=O)C1=CC=C(N(C)C2=CC=CC=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 67, 67, 29, 67, 29, 29, 29, 6, 1, 6, 1, 1, 1, 1, 1, 1, 29, 29, 119, 140, 140, 201, 201, 201, 201, 201, 119, 67, 29, 29, 6, 6, 6, 1, 1, 1, 1, 1, 29] 201 rigid atoms, others: [37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42]) total number of confs: 885 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919771 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919771 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919771/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919771 Building REAL300004919772 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919772' /scratch/stefan/7775247/working/building/REAL300004919772 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919772 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919772/0 /scratch/stefan/7775247/working/building/REAL300004919772 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 777) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/777 `/scratch/stefan/7775247/working/3D/777' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(OCC2=CC=CN=C2)C=C1)C(=O)[O-]) `REAL300004919772.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919772 none CC#CCC(NC(=O)C=CC1=CC=C(OCC2=CC=CN=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 11, 11, 3, 11, 3, 1, 1, 1, 1, 1, 1, 2, 2, 15, 15, 15, 15, 15, 1, 1, 21, 34, 34, 42, 42, 42, 42, 42, 21, 11, 3, 3, 1, 1, 2, 2, 15, 15, 15, 15, 1, 1] 201 rigid atoms, others: [45, 36, 37, 9, 10, 11, 12, 13, 14, 44, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43]) total number of confs: 243 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919772 none CC#CCC(NC(=O)C=CC1=CC=C(OCC2=CC=CN=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 85, 85, 30, 85, 30, 15, 14, 15, 15, 8, 8, 1, 1, 1, 1, 1, 1, 1, 15, 15, 131, 164, 164, 201, 201, 201, 201, 201, 131, 85, 30, 30, 15, 15, 8, 8, 1, 1, 1, 1, 15, 15] 201 rigid atoms, others: [40, 41, 42, 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, 44, 45]) total number of confs: 1000 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919772 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919772 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919772/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919772 Building REAL300004919773 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919773' /scratch/stefan/7775247/working/building/REAL300004919773 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919773 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919773/0 /scratch/stefan/7775247/working/building/REAL300004919773 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/778 `/scratch/stefan/7775247/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C)=C(OCC2=CC=CN=C2)C(C)=C1)C(=O)[O-]) `REAL300004919773.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919773 none CC#CCC(NC(=O)C1=CC(C)=C(OCC2=CC=CN=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 5, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 2, 8, 26, 26, 26, 26, 26, 1, 1, 1, 13, 21, 21, 34, 34, 34, 34, 34, 13, 5, 1, 2, 2, 2, 8, 8, 26, 26, 26, 26, 2, 2, 2, 1] 201 rigid atoms, others: [34, 6, 8, 9, 10, 11, 12, 13, 47, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919773 none CC#CCC(NC(=O)C1=CC(C)=C(OCC2=CC=CN=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 5, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 128, 74, 74, 26, 74, 22, 26, 26, 26, 22, 8, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 128, 152, 152, 201, 201, 201, 201, 201, 128, 74, 26, 27, 27, 27, 8, 8, 1, 1, 1, 1, 27, 27, 27, 26] 201 rigid atoms, others: [40, 41, 42, 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, 44, 45, 46, 47]) total number of confs: 965 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919773 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919773 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919773/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919773 Building REAL300004919774 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919774' /scratch/stefan/7775247/working/building/REAL300004919774 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919774 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919774/0 /scratch/stefan/7775247/working/building/REAL300004919774 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 779) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/779 `/scratch/stefan/7775247/working/3D/779' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OCC2=CC=CN=C2)C(OCC)=C1)C(=O)[O-]) `REAL300004919774.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919774 none CC#CCC(NC(=O)C1=CC=C(OCC2=CC=CN=C2)C(OCC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 12, 5, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 5, 5, 1, 5, 1, 1, 1, 1, 1, 7, 12, 37, 37, 37, 37, 37, 1, 1, 6, 8, 1, 7, 9, 9, 13, 13, 13, 13, 13, 7, 5, 1, 1, 12, 12, 37, 37, 37, 37, 8, 8, 8, 8, 8, 1] 201 rigid atoms, others: [35, 36, 6, 8, 9, 10, 11, 12, 48, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919774 none CC#CCC(NC(=O)C1=CC=C(OCC2=CC=CN=C2)C(OCC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 1, 1, 12, 5, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [195, 195, 195, 105, 97, 97, 37, 97, 34, 37, 37, 25, 6, 1, 1, 1, 1, 1, 1, 1, 37, 37, 61, 65, 37, 105, 124, 124, 195, 195, 195, 195, 195, 105, 97, 37, 37, 6, 6, 1, 1, 1, 1, 65, 65, 65, 65, 65, 37] 201 rigid atoms, others: [39, 40, 41, 42, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 48]) total number of confs: 941 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919774 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919774 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919774/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919774 Building REAL300004919775 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919775' /scratch/stefan/7775247/working/building/REAL300004919775 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919775 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919775/0 /scratch/stefan/7775247/working/building/REAL300004919775 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/780 `/scratch/stefan/7775247/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OCC(=O)NC(C)C)C(OC)=C1)C(=O)[O-]) `REAL300004919775.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919775 none CC#CCC(NC(=O)C1=CC=C(OCC(=O)NC(C)C)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 7, 19, 28, 28, 28, 34, 34, 1, 1, 3, 1, 9, 15, 15, 21, 21, 21, 21, 21, 9, 5, 1, 1, 19, 19, 28, 34, 34, 34, 34, 34, 34, 34, 3, 3, 3, 1] 201 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 49, 20, 21, 23] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919775 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919775 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919775/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919775 Building REAL300004919776 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919776' /scratch/stefan/7775247/working/building/REAL300004919776 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919776 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919776/0 /scratch/stefan/7775247/working/building/REAL300004919776 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 781) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/781 `/scratch/stefan/7775247/working/3D/781' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CNC(=O)COC1=CC=CC=C1)C(=O)[O-]) `REAL300004919776.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919776 none CC#CCC(NC(=O)CNC(=O)COC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 169, 158, 158, 80, 158, 35, 35, 13, 35, 3, 1, 1, 1, 1, 1, 1, 1, 169, 187, 187, 201, 201, 201, 201, 201, 169, 158, 80, 80, 35, 13, 13, 1, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 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]) total number of confs: 829 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919776 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919776 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919776/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919776 Building REAL300004919777 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919777' /scratch/stefan/7775247/working/building/REAL300004919777 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919777 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919777/0 /scratch/stefan/7775247/working/building/REAL300004919777 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/782 `/scratch/stefan/7775247/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CNC(=O)C1=C(Cl)C2=CC=CC=C2S1)C(=O)[O-]) `REAL300004919777.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919777 none CC#CCC(NC(=O)CNC(=O)C1=C(Cl)C2=CC=CC=C2S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 11, 1, 1, 16, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 129, 81, 81, 20, 81, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 129, 170, 170, 201, 201, 201, 201, 201, 129, 81, 20, 20, 5, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 1011 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919777 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919777 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919777/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919777 Building REAL300004919778 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919778' /scratch/stefan/7775247/working/building/REAL300004919778 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919778 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919778/0 /scratch/stefan/7775247/working/building/REAL300004919778 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 783) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/783 `/scratch/stefan/7775247/working/3D/783' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(NC(=O)C1=CC=C(OCC)C=C1)C(C)C)C(=O)[O-]) `REAL300004919778.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919778 none CC#CCC(NC(=O)C(NC(=O)C1=CC=C(OCC)C=C1)C(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 43, 26, 26, 7, 26, 3, 3, 1, 3, 1, 1, 1, 1, 1, 6, 15, 1, 1, 7, 16, 18, 43, 58, 58, 88, 88, 88, 88, 88, 43, 26, 7, 3, 1, 1, 15, 15, 15, 15, 15, 1, 1, 18, 18, 18, 18, 18, 18, 18] 201 rigid atoms, others: [36, 37, 44, 10, 43, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 526 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919778 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919778 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919778/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919778 Building REAL300004919779 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919779' /scratch/stefan/7775247/working/building/REAL300004919779 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919779 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919779/0 /scratch/stefan/7775247/working/building/REAL300004919779 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/784 `/scratch/stefan/7775247/working/3D/784' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC=C2C)C(C)=C1)C(=O)[O-]) `REAL300004919779.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919779 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC=C2C)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [79, 79, 79, 39, 12, 12, 1, 12, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 3, 1, 1, 1, 39, 53, 53, 79, 79, 79, 79, 79, 39, 12, 2, 2, 2, 3, 3, 2, 3, 3, 3, 3, 2, 2, 2, 1] 141 rigid atoms, others: [6, 8, 9, 10, 11, 12, 45, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 390 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919779 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=CC=C2C)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [141, 141, 141, 72, 24, 24, 3, 24, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 72, 97, 97, 141, 141, 141, 141, 141, 72, 24, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3] 141 rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 669 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919779 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919779 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919779/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919779 Building REAL300004919780 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919780' /scratch/stefan/7775247/working/building/REAL300004919780 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919780 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919780/0 /scratch/stefan/7775247/working/building/REAL300004919780 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 785) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/785 `/scratch/stefan/7775247/working/3D/785' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C2C(=O)N3CCCCCC3=NC2=C1)C(=O)[O-]) `REAL300004919780.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919780 none CC#CCC(NC(=O)C1=CC=C2C(=O)N3CCCCCC3=NC2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [59, 59, 59, 28, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 38, 38, 59, 59, 59, 59, 59, 28, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 59 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46] set([0, 1, 2, 3, 4, 5, 7, 33, 32, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 277 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919780 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919780 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919780/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919780 Building REAL300004919781 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919781' /scratch/stefan/7775247/working/building/REAL300004919781 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919781 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919781/0 /scratch/stefan/7775247/working/building/REAL300004919781 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/786 `/scratch/stefan/7775247/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=C(S1)N(CC1=CC=CC=C1)N=C2C)C(=O)[O-]) `REAL300004919781.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919781 none CC#CCC(NC(=O)C1=CC2=C(S1)N(CC1=CC=CC=C1)N=C2C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 14, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 26, 11, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15, 10, 15, 15, 1, 1, 1, 26, 41, 41, 49, 49, 49, 49, 49, 26, 11, 1, 7, 7, 15, 15, 15, 15, 15, 2, 2, 2] 201 rigid atoms, others: [34, 6, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 317 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919781 none CC#CCC(NC(=O)C1=CC2=C(S1)N(CC1=CC=CC=C1)N=C2C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 14, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 126, 64, 63, 15, 63, 15, 15, 15, 15, 15, 4, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 126, 160, 160, 201, 201, 201, 201, 201, 126, 64, 15, 4, 4, 1, 1, 1, 1, 1, 16, 16, 16] 201 rigid atoms, others: [37, 38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44]) total number of confs: 963 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919781 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919781 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919781/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919781 Building REAL300004919782 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919782' /scratch/stefan/7775247/working/building/REAL300004919782 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919782 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919782/0 /scratch/stefan/7775247/working/building/REAL300004919782 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 787) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/787 `/scratch/stefan/7775247/working/3D/787' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCNS(=O)(=O)C=CC1=CC=CC=C1)C(=O)[O-]) `REAL300004919782.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919782 none CC#CCC(NC(=O)CCNS(=O)(=O)C=CC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 185, 185, 104, 185, 94, 46, 29, 5, 29, 29, 5, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 185, 104, 104, 94, 94, 46, 5, 5, 1, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 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]) total number of confs: 761 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919782 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919782 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919782/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919782 Building REAL300004919783 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919783' /scratch/stefan/7775247/working/building/REAL300004919783 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919783 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919783/0 /scratch/stefan/7775247/working/building/REAL300004919783 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/788 `/scratch/stefan/7775247/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)C2=C(O1)C1=C(C=CC=C1)C=C2)C(=O)[O-]) `REAL300004919783.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919783 none CC#CCC(NC(=O)C1=C(C)C2=C(O1)C1=C(C=CC=C1)C=C2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 5, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 37, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 47, 47, 66, 66, 66, 66, 66, 37, 11, 2, 2, 2, 1, 1, 1, 1, 1, 1] 66 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 34, 33, 32, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 324 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919783 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919783 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919783/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919783 Building REAL300004919784 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919784' /scratch/stefan/7775247/working/building/REAL300004919784 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919784 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919784/0 /scratch/stefan/7775247/working/building/REAL300004919784 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 789) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/789 `/scratch/stefan/7775247/working/3D/789' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C)=NC2=CC=C(C)C=C21)C(=O)[O-]) `REAL300004919784.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919784 none CC#CCC(NC(=O)C1=CC(C)=NC2=CC=C(C)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 5, 8, 1, 1, 1, 1, 5, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 36, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 53, 53, 89, 89, 89, 89, 89, 36, 9, 1, 2, 2, 2, 1, 1, 2, 2, 2, 1] 89 rigid atoms, others: [34, 35, 6, 39, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 36, 37, 38]) total number of confs: 420 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919784 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919784 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919784/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919784 Building REAL300004919785 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919785' /scratch/stefan/7775247/working/building/REAL300004919785 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919785 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919785/0 /scratch/stefan/7775247/working/building/REAL300004919785 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/790 `/scratch/stefan/7775247/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C2=CC=C(C)C=C2C)=NC2=CC=CC=C21)C(=O)[O-]) `REAL300004919785.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919785 none CC#CCC(NC(=O)C1=CC(C2=CC=C(C)C=C2C)=NC2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 29, 9, 9, 1, 9, 1, 1, 1, 1, 9, 9, 1, 1, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 29, 49, 49, 63, 63, 63, 63, 63, 29, 9, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1] 201 rigid atoms, others: [36, 6, 49, 8, 9, 10, 11, 48, 24, 19, 20, 21, 22, 23, 46, 25, 47] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 379 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919785 none CC#CCC(NC(=O)C1=CC(C2=CC=C(C)C=C2C)=NC2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 123, 53, 53, 9, 53, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 123, 153, 153, 201, 201, 201, 201, 201, 123, 53, 9, 1, 1, 2, 2, 2, 1, 2, 2, 2, 9, 9, 9, 9] 201 rigid atoms, others: [37, 38, 10, 11, 12, 13, 14, 15, 16, 17, 18, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 969 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919785 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919785 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919785/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919785 Building REAL300004919786 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919786' /scratch/stefan/7775247/working/building/REAL300004919786 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919786 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919786/0 /scratch/stefan/7775247/working/building/REAL300004919786 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 791) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/791 `/scratch/stefan/7775247/working/3D/791' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCNS(=O)(=O)C1=CC=CC=C1)C(=O)[O-]) `REAL300004919786.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919786 none CC#CCC(NC(=O)CCNS(=O)(=O)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1] 3 rigid atoms, others: [35, 36, 37, 38, 39, 11, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919786 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919786 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919786/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919786 Building REAL300004919787 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919787' /scratch/stefan/7775247/working/building/REAL300004919787 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919787 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919787/0 /scratch/stefan/7775247/working/building/REAL300004919787 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/792 `/scratch/stefan/7775247/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=C(Cl)N(CC2=CC=CC=C2)N=C1C)C(=O)[O-]) `REAL300004919787.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919787 none CC#CCC(NC(=O)C=CC1=C(Cl)N(CC2=CC=CC=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 16, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 82, 41, 41, 7, 41, 7, 1, 1, 1, 1, 1, 1, 5, 10, 10, 8, 10, 10, 1, 1, 1, 82, 82, 82, 103, 103, 103, 103, 103, 82, 41, 7, 7, 5, 5, 10, 10, 10, 10, 10, 2, 2, 2] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 459 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919787 none CC#CCC(NC(=O)C=CC1=C(Cl)N(CC2=CC=CC=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 16, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 130, 130, 39, 130, 39, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 194, 194, 194, 201, 201, 201, 201, 201, 194, 130, 39, 39, 4, 4, 1, 1, 1, 1, 1, 10, 10, 10] 201 rigid atoms, others: [38, 39, 40, 41, 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, 43, 44, 45]) total number of confs: 743 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919787 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919787 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919787/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919787 Building REAL300004919788 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919788' /scratch/stefan/7775247/working/building/REAL300004919788 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919788 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919788/0 /scratch/stefan/7775247/working/building/REAL300004919788 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 793) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/793 `/scratch/stefan/7775247/working/3D/793' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CNC(=O)CC12CC3CC(CC(C3)C1)C2)C(=O)[O-]) `REAL300004919788.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919788 none CC#CCC(NC(=O)CNC(=O)CC12CC3CC(CC(C3)C1)C2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 134, 83, 83, 26, 83, 8, 8, 3, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 134, 167, 167, 201, 201, 201, 201, 201, 134, 83, 26, 26, 8, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 991 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919788 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919788 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919788/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919788 Building REAL300004919789 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919789' /scratch/stefan/7775247/working/building/REAL300004919789 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919789 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919789/0 /scratch/stefan/7775247/working/building/REAL300004919789 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/794 `/scratch/stefan/7775247/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C12CCC(=O)N1C1=CC=CC=C1S2)C(=O)[O-]) `REAL300004919789.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919789 none CC#CCC(NC(=O)C12CCC(=O)N1C1=CC=CC=C1S2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 46, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 59, 59, 90, 90, 90, 90, 90, 46, 13, 1, 1, 1, 1, 1, 1, 1, 1] 90 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 7, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 397 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919789 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919789 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919789/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919789 Building REAL300004919790 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919790' /scratch/stefan/7775247/working/building/REAL300004919790 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919790 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919790/0 /scratch/stefan/7775247/working/building/REAL300004919790 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 795) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/795 `/scratch/stefan/7775247/working/3D/795' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CSC1=NN=C(C2CC2)N1CC1=CC=CC=C1)C(=O)[O-]) `REAL300004919790.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919790 none CC#CCC(NC(=O)CSC1=NN=C(C2CC2)N1CC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 33, 20, 20, 12, 20, 6, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 6, 12, 12, 6, 12, 12, 33, 50, 50, 73, 73, 73, 73, 73, 33, 20, 12, 12, 8, 8, 8, 8, 8, 6, 6, 12, 12, 6, 12, 12] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 434 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919790 none CC#CCC(NC(=O)CSC1=NN=C(C2CC2)N1CC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [159, 159, 159, 92, 57, 57, 42, 57, 27, 12, 12, 12, 12, 12, 12, 31, 31, 5, 1, 1, 1, 1, 1, 1, 1, 92, 125, 125, 159, 159, 159, 159, 159, 92, 57, 42, 42, 31, 31, 31, 31, 31, 5, 5, 1, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 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]) total number of confs: 892 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919790 none CC#CCC(NC(=O)CSC1=NN=C(C2CC2)N1CC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 14, 1, 8, 8, 1, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [152, 152, 152, 106, 60, 60, 42, 60, 23, 8, 8, 8, 8, 1, 1, 1, 1, 8, 8, 20, 31, 31, 20, 31, 31, 106, 128, 128, 152, 152, 152, 152, 152, 106, 60, 42, 42, 1, 1, 1, 1, 1, 20, 20, 31, 31, 20, 31, 31] 201 rigid atoms, others: [37, 38, 39, 40, 41, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 854 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919790 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919790 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919790/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919790 Building REAL300004919791 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919791' /scratch/stefan/7775247/working/building/REAL300004919791 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919791 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919791/0 /scratch/stefan/7775247/working/building/REAL300004919791 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/796 `/scratch/stefan/7775247/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCNS(=O)(=O)C1=C(C)C=C(C)C=C1C)C(=O)[O-]) `REAL300004919791.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919791 none CC#CCC(NC(=O)CCNS(=O)(=O)C1=C(C)C=C(C)C=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 8, 14, 11, 11, 1, 1, 5, 1, 1, 5, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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, 13, 12, 12, 8, 12, 6, 3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 15, 15, 15, 15, 15, 13, 12, 8, 8, 6, 6, 3, 2, 2, 2, 1, 2, 2, 2, 1, 2, 2, 2] 15 rigid atoms, others: [41, 11, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 46, 47, 48]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919791 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919791 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919791/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919791 Building REAL300004919792 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919792' /scratch/stefan/7775247/working/building/REAL300004919792 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919792 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919792/0 /scratch/stefan/7775247/working/building/REAL300004919792 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 797) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/797 `/scratch/stefan/7775247/working/3D/797' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(NC(=O)C2CC3=CC=CC=C3O2)=C1)C(=O)[O-]) `REAL300004919792.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919792 none CC#CCC(NC(=O)C1=CC=CC(NC(=O)C2CC3=CC=CC=C3O2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 1, 14, 22, 22, 37, 37, 37, 37, 37, 14, 5, 1, 1, 1, 6, 19, 19, 19, 19, 19, 19, 19, 1] 201 rigid atoms, others: [36, 37, 6, 8, 9, 10, 11, 12, 13, 47, 25, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45, 46]) 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: REAL300004919792 none CC#CCC(NC(=O)C1=CC=CC(NC(=O)C2CC3=CC=CC=C3O2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 53, 53, 19, 53, 19, 19, 19, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 118, 151, 151, 201, 201, 201, 201, 201, 118, 53, 19, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 19] 201 rigid atoms, others: [40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 47]) total number of confs: 965 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919792 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919792 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919792/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919792 Building REAL300004919793 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919793' /scratch/stefan/7775247/working/building/REAL300004919793 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919793 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919793/0 /scratch/stefan/7775247/working/building/REAL300004919793 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/798 `/scratch/stefan/7775247/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC)C(OC2CCCC2)=C1)C(=O)[O-]) `REAL300004919793.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919793 none CC#CCC(NC(=O)C1=CC=C(OC)C(OC2CCCC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 12, 5, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 3, 1, 1, 9, 19, 19, 19, 19, 1, 13, 21, 21, 35, 35, 35, 35, 35, 13, 5, 1, 1, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 14, 15, 21, 46] set([0, 1, 2, 3, 4, 5, 7, 13, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919793 none CC#CCC(NC(=O)C1=CC=C(OC)C(OC2CCCC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 12, 5, 5, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [190, 190, 190, 107, 58, 58, 19, 58, 19, 19, 19, 19, 19, 28, 6, 1, 1, 1, 1, 1, 1, 19, 107, 141, 141, 190, 190, 190, 190, 190, 107, 58, 19, 19, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46]) total number of confs: 923 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919793 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919793 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919793/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919793 Building REAL300004919794 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919794' /scratch/stefan/7775247/working/building/REAL300004919794 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919794 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919794/0 /scratch/stefan/7775247/working/building/REAL300004919794 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 799) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/799 `/scratch/stefan/7775247/working/3D/799' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(CCC)N(C2=CC=CC=C2)N=C1)C(=O)[O-]) `REAL300004919794.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919794 none CC#CCC(NC(=O)C1=C(CCC)N(C2=CC=CC=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 28, 11, 11, 1, 11, 1, 1, 1, 5, 10, 1, 1, 5, 5, 1, 5, 5, 1, 1, 28, 47, 47, 76, 76, 76, 76, 76, 28, 12, 5, 5, 10, 10, 10, 10, 10, 5, 5, 5, 5, 5, 1] 161 rigid atoms, others: [6, 8, 9, 10, 44, 13, 14, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 441 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919794 none CC#CCC(NC(=O)C1=C(CCC)N(C2=CC=CC=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 53, 25, 25, 5, 25, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 5, 5, 53, 80, 80, 118, 118, 118, 118, 118, 53, 25, 7, 7, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 5] 161 rigid atoms, others: [39, 40, 41, 42, 43, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44]) total number of confs: 611 number of broken/clashed sets: 78 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919794 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919794 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919794/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919794 Building REAL300004919795 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919795' /scratch/stefan/7775247/working/building/REAL300004919795 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919795 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919795/0 /scratch/stefan/7775247/working/building/REAL300004919795 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/800 `/scratch/stefan/7775247/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)C2=C(CC(C)(C)CC2=O)N1)C(=O)[O-]) `REAL300004919795.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919795 none CC#CCC(NC(=O)C1=C(C)C2=C(CC(C)(C)CC2=O)N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 1, 1, 5, 5, 5, 5, 5, 1, 11, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 37, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 53, 53, 73, 73, 73, 73, 73, 37, 13, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1] 73 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 43, 44, 42] set([0, 1, 2, 3, 4, 5, 7, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 385 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919795 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919795 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919795/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919795 Building REAL300004919796 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919796' /scratch/stefan/7775247/working/building/REAL300004919796 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919796 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919796/0 /scratch/stefan/7775247/working/building/REAL300004919796 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 801) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/801 `/scratch/stefan/7775247/working/3D/801' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C2C=NN(C(C)C)C2=NC(C2=CC=CC=C2)=C1)C(=O)[O-]) `REAL300004919796.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919796 none CC#CCC(NC(=O)C1=C2C=NN(C(C)C)C2=NC(C2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 29, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 29, 48, 48, 81, 81, 81, 81, 81, 29, 12, 1, 8, 8, 8, 8, 8, 8, 8, 6, 6, 1, 6, 6, 1] 201 rigid atoms, others: [36, 6, 49, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 25] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 444 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919796 none CC#CCC(NC(=O)C1=C2C=NN(C(C)C)C2=NC(C2=CC=CC=C2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [155, 155, 155, 92, 44, 44, 6, 44, 6, 6, 6, 6, 6, 6, 26, 26, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 92, 135, 135, 155, 155, 155, 155, 155, 92, 44, 6, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 6] 201 rigid atoms, others: [44, 45, 46, 47, 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, 49]) total number of confs: 883 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919796 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919796 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919796/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919796 Building REAL300004919797 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919797' /scratch/stefan/7775247/working/building/REAL300004919797 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919797 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919797/0 /scratch/stefan/7775247/working/building/REAL300004919797 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/802 `/scratch/stefan/7775247/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C2C=NN(C(C)C)C2=NC(C2CC2)=C1)C(=O)[O-]) `REAL300004919797.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919797 none CC#CCC(NC(=O)C1=C2C=NN(C(C)C)C2=NC(C2CC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 8, 1, 5, 5, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 29, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 6, 1, 1, 1, 1, 11, 11, 1, 29, 47, 47, 82, 82, 82, 82, 82, 29, 12, 1, 6, 6, 6, 6, 7, 7, 7, 11, 11, 11, 11, 11, 1] 201 rigid atoms, others: [33, 6, 8, 9, 10, 11, 12, 13, 46, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 443 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919797 none CC#CCC(NC(=O)C1=C2C=NN(C(C)C)C2=NC(C2CC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 1, 8, 1, 5, 5, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [174, 174, 174, 102, 56, 56, 11, 56, 11, 11, 11, 11, 11, 11, 39, 39, 11, 11, 1, 1, 1, 1, 11, 102, 139, 139, 174, 174, 174, 174, 174, 102, 56, 11, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 11] 201 rigid atoms, others: [41, 42, 43, 44, 45, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46]) total number of confs: 915 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919797 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919797 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919797/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919797 Building REAL300004919798 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919798' /scratch/stefan/7775247/working/building/REAL300004919798 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919798 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919798/0 /scratch/stefan/7775247/working/building/REAL300004919798 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 803) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/803 `/scratch/stefan/7775247/working/3D/803' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1OC2=CC=CC=C2NC1=O)C(=O)[O-]) `REAL300004919798.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919798 none CC#CCC(NC(=O)CC1OC2=CC=CC=C2NC1=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 101, 44, 44, 8, 44, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 101, 138, 138, 201, 201, 201, 201, 201, 101, 44, 8, 8, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 983 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919798 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919798 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919798/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919798 Building REAL300004919799 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919799' /scratch/stefan/7775247/working/building/REAL300004919799 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919799 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919799/0 /scratch/stefan/7775247/working/building/REAL300004919799 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/804 `/scratch/stefan/7775247/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C2CC2)=NC2=CC=CC=C21)C(=O)[O-]) `REAL300004919799.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919799 none CC#CCC(NC(=O)C1=CC(C2CC2)=NC2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 32, 9, 9, 1, 9, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 32, 56, 56, 105, 105, 105, 105, 105, 32, 9, 1, 11, 11, 11, 11, 11, 1, 1, 1, 1] 201 rigid atoms, others: [37, 6, 39, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 40, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 524 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919799 none CC#CCC(NC(=O)C1=CC(C2CC2)=NC2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 56, 56, 11, 56, 11, 11, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 114, 150, 150, 201, 201, 201, 201, 201, 114, 56, 11, 1, 1, 1, 1, 1, 11, 11, 11, 11] 201 rigid atoms, others: [32, 33, 34, 35, 36, 10, 11, 12, 13] 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, 37, 38, 39, 40]) total number of confs: 933 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919799 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919799 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919799/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919799 Building REAL300004919800 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919800' /scratch/stefan/7775247/working/building/REAL300004919800 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919800 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919800/0 /scratch/stefan/7775247/working/building/REAL300004919800 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 805) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/805 `/scratch/stefan/7775247/working/3D/805' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC(NC(C)=O)C1=CC=C(Br)C=C1)C(=O)[O-]) `REAL300004919800.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919800 none CC#CCC(NC(=O)CC(NC(C)=O)C1=CC=C(Br)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 5, 8, 1, 5, 11, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 165, 165, 79, 39, 39, 11, 39, 4, 1, 4, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 79, 109, 109, 165, 165, 165, 165, 165, 79, 39, 11, 11, 4, 6, 6, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 9, 14, 15, 16, 17, 18, 19, 20, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 814 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919800 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919800 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919800/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919800 Building REAL300004919801 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919801' /scratch/stefan/7775247/working/building/REAL300004919801 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919801 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919801/0 /scratch/stefan/7775247/working/building/REAL300004919801 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/806 `/scratch/stefan/7775247/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C(C)C)=NC2=CC=CC=C21)C(=O)[O-]) `REAL300004919801.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919801 none CC#CCC(NC(=O)C1=CC(C(C)C)=NC2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 111, 40, 9, 9, 1, 9, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 40, 60, 60, 111, 111, 111, 111, 111, 40, 9, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1] 176 rigid atoms, others: [6, 39, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 41, 40, 42, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 510 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919801 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919801 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919801/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919801 Building REAL300004919802 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919802' /scratch/stefan/7775247/working/building/REAL300004919802 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919802 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919802/0 /scratch/stefan/7775247/working/building/REAL300004919802 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 807) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/807 `/scratch/stefan/7775247/working/3D/807' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C(C)C)C(C(C)=O)=C(C)N1)C(=O)[O-]) `REAL300004919802.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919802 none CC#CCC(NC(=O)C1=C(C(C)C)C(C(C)=O)=C(C)N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 5, 5, 1, 1, 5, 11, 1, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 38, 12, 12, 1, 12, 1, 1, 1, 3, 3, 1, 1, 11, 11, 1, 1, 1, 38, 59, 59, 105, 105, 105, 105, 105, 38, 12, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 2, 2, 2, 1] 186 rigid atoms, others: [6, 8, 9, 10, 43, 13, 14, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 530 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919802 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919802 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919802/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919802 Building REAL300004919803 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919803' /scratch/stefan/7775247/working/building/REAL300004919803 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919803 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919803/0 /scratch/stefan/7775247/working/building/REAL300004919803 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/808 `/scratch/stefan/7775247/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C2=CC=CC=C2)OC(C)=N1)C(=O)[O-]) `REAL300004919803.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919803 none CC#CCC(NC(=O)C1=C(C2=CC=CC=C2)OC(C)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 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: [135, 135, 135, 51, 13, 13, 1, 13, 1, 1, 1, 6, 6, 1, 6, 6, 1, 1, 1, 1, 51, 73, 73, 135, 135, 135, 135, 135, 51, 13, 6, 6, 3, 6, 6, 2, 2, 2] 177 rigid atoms, others: [6, 8, 9, 10, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 620 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919803 none CC#CCC(NC(=O)C1=C(C2=CC=CC=C2)OC(C)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 5, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [177, 177, 177, 94, 40, 40, 6, 40, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 94, 122, 122, 177, 177, 177, 177, 177, 94, 40, 1, 1, 1, 1, 1, 6, 6, 6] 177 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37]) total number of confs: 815 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919803 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919803 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919803/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919803 Building REAL300004919804 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919804' /scratch/stefan/7775247/working/building/REAL300004919804 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919804 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919804/0 /scratch/stefan/7775247/working/building/REAL300004919804 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 809) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/809 `/scratch/stefan/7775247/working/3D/809' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(OC)=C(Br)S1)C(=O)[O-]) `REAL300004919804.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919804 none CC#CCC(NC(=O)C1=CC(OC)=C(Br)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'Br', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 12, 5, 1, 17, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 47, 13, 12, 1, 12, 1, 1, 1, 1, 3, 1, 1, 1, 47, 69, 69, 112, 112, 112, 112, 112, 47, 13, 1, 4, 4, 4] 128 rigid atoms, others: [6, 8, 9, 10, 11, 13, 14, 15, 26] set([0, 1, 2, 3, 4, 5, 7, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29]) total number of confs: 540 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919804 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919804 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919804/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919804 Building REAL300004919805 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919805' /scratch/stefan/7775247/working/building/REAL300004919805 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919805 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919805/0 /scratch/stefan/7775247/working/building/REAL300004919805 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/810 `/scratch/stefan/7775247/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CN(CCC1=CC=CC=C1)C(C)=O)C(=O)[O-]) `REAL300004919805.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919805 none CC#CCC(NC(=O)CN(CCC1=CC=CC=C1)C(C)=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 11, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 2, 2, 7, 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: [87, 87, 87, 64, 35, 35, 16, 35, 9, 6, 4, 1, 1, 1, 1, 1, 1, 1, 9, 13, 13, 64, 69, 69, 87, 87, 87, 87, 87, 64, 35, 16, 16, 6, 6, 4, 4, 1, 1, 1, 1, 1, 13, 13, 13] 90 rigid atoms, others: [37, 38, 39, 40, 41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44]) total number of confs: 421 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919805 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919805 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919805/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919805 Building REAL300004919806 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919806' /scratch/stefan/7775247/working/building/REAL300004919806 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919806 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919806/0 /scratch/stefan/7775247/working/building/REAL300004919806 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 811) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/811 `/scratch/stefan/7775247/working/3D/811' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2Cl)C=C1C)C(=O)[O-]) `REAL300004919806.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919806 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2Cl)C=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 30, 10, 10, 1, 10, 1, 1, 1, 1, 12, 12, 11, 12, 12, 12, 1, 1, 1, 30, 43, 43, 76, 76, 76, 76, 76, 30, 10, 12, 12, 11, 12, 1, 2, 2, 2] 201 rigid atoms, others: [35, 6, 8, 9, 10, 11, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919806 none CC#CCC(NC(=O)C1=NN(C2=CC=CC=C2Cl)C=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 102, 51, 51, 12, 51, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 102, 139, 139, 201, 201, 201, 201, 201, 102, 51, 1, 1, 1, 1, 12, 12, 12, 12] 201 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 939 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919806 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919806 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919806/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919806 Building REAL300004919807 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919807' /scratch/stefan/7775247/working/building/REAL300004919807 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919807 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919807/0 /scratch/stefan/7775247/working/building/REAL300004919807 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/812 `/scratch/stefan/7775247/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2CCOCC2)N=C1)C(=O)[O-]) `REAL300004919807.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919807 none CC#CCC(NC(=O)C1=C(C)N(C2CCOCC2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 8, 5, 5, 5, 12, 5, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 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: [102, 102, 102, 49, 13, 13, 1, 13, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 49, 69, 69, 102, 102, 102, 102, 102, 49, 13, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1] 177 rigid atoms, others: [6, 8, 9, 10, 11, 12, 18, 19, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 494 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: REAL300004919807 none CC#CCC(NC(=O)C1=C(C)N(C2CCOCC2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 8, 5, 5, 5, 12, 5, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [177, 177, 177, 103, 42, 42, 6, 42, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 103, 128, 128, 177, 177, 177, 177, 177, 103, 42, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6] 177 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42]) total number of confs: 783 number of broken/clashed sets: 51 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919807 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919807 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919807/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919807 Building REAL300004919808 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919808' /scratch/stefan/7775247/working/building/REAL300004919808 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919808 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919808/0 /scratch/stefan/7775247/working/building/REAL300004919808 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 813) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/813 `/scratch/stefan/7775247/working/3D/813' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C(CC)CC)C(C)=C1)C(=O)[O-]) `REAL300004919808.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919808 none CC#CCC(NC(=O)C1=NN(C(CC)CC)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 8, 8, 5, 5, 5, 5, 5, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 30, 12, 12, 1, 12, 1, 1, 1, 1, 3, 6, 3, 5, 1, 1, 1, 30, 48, 48, 89, 89, 89, 89, 89, 30, 12, 3, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6, 2, 2, 2, 1] 175 rigid atoms, others: [43, 6, 8, 9, 10, 11, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 465 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919808 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919808 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919808/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919808 Building REAL300004919809 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919809' /scratch/stefan/7775247/working/building/REAL300004919809 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919809 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919809/0 /scratch/stefan/7775247/working/building/REAL300004919809 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/814 `/scratch/stefan/7775247/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CC1C1=CC=CC=C1Cl)C(=O)[O-]) `REAL300004919809.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919809 none CC#CCC(NC(=O)C1CC1C1=CC=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 111, 41, 12, 12, 1, 12, 1, 1, 1, 1, 6, 6, 2, 6, 6, 6, 41, 63, 63, 111, 111, 111, 111, 111, 41, 12, 1, 1, 1, 1, 6, 6, 2, 6] 201 rigid atoms, others: [6, 8, 9, 10, 11, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 535 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919809 none CC#CCC(NC(=O)C1CC1C1=CC=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 51, 51, 6, 51, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 114, 153, 153, 201, 201, 201, 201, 201, 114, 51, 6, 6, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 974 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919809 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919809 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919809/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919809 Building REAL300004919810 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919810' /scratch/stefan/7775247/working/building/REAL300004919810 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919810 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919810/0 /scratch/stefan/7775247/working/building/REAL300004919810 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 815) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/815 `/scratch/stefan/7775247/working/3D/815' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=C(F)C=C2)C=C1C)C(=O)[O-]) `REAL300004919810.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919810 none CC#CCC(NC(=O)C1=NN(C2=CC=C(F)C=C2)C=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [72, 72, 72, 31, 11, 11, 1, 11, 1, 1, 1, 1, 4, 4, 3, 3, 4, 4, 1, 1, 1, 31, 46, 46, 72, 72, 72, 72, 72, 31, 11, 4, 4, 4, 4, 1, 2, 2, 2] 74 rigid atoms, others: [35, 6, 8, 9, 10, 11, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 366 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919810 none CC#CCC(NC(=O)C1=NN(C2=CC=C(F)C=C2)C=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [74, 74, 74, 41, 19, 19, 4, 19, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 41, 53, 53, 74, 74, 74, 74, 74, 41, 19, 1, 1, 1, 1, 4, 4, 4, 4] 74 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 347 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919810 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919810 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919810/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919810 Building REAL300004919811 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919811' /scratch/stefan/7775247/working/building/REAL300004919811 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919811 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919811/0 /scratch/stefan/7775247/working/building/REAL300004919811 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/816 `/scratch/stefan/7775247/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=CC(Cl)=C1OCC)C(=O)[O-]) `REAL300004919811.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919811 none CC#CCC(NC(=O)CC1=CC=CC(Cl)=C1OCC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 12, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [145, 145, 145, 70, 33, 33, 6, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 70, 103, 103, 145, 145, 145, 145, 145, 70, 33, 6, 6, 1, 1, 1, 8, 8, 9, 9, 9] 201 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 764 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919811 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919811 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919811/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919811 Building REAL300004919812 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919812' /scratch/stefan/7775247/working/building/REAL300004919812 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919812 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919812/0 /scratch/stefan/7775247/working/building/REAL300004919812 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 817) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/817 `/scratch/stefan/7775247/working/3D/817' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(S(C)(=O)=O)=CC=C1CC)C(=O)[O-]) `REAL300004919812.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919812 none CC#CCC(NC(=O)C1=CC(S(C)(=O)=O)=CC=C1CC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 14, 5, 11, 11, 1, 1, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 28, 9, 9, 1, 9, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 6, 28, 46, 46, 75, 75, 75, 75, 75, 28, 9, 1, 3, 3, 3, 1, 1, 6, 6, 6, 6, 6] 201 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 36, 37, 38, 39, 40]) total number of confs: 400 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919812 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919812 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919812/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919812 Building REAL300004919813 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919813' /scratch/stefan/7775247/working/building/REAL300004919813 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919813 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919813/0 /scratch/stefan/7775247/working/building/REAL300004919813 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/818 `/scratch/stefan/7775247/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(C2CCOC2)=C1)C(=O)[O-]) `REAL300004919813.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919813 none CC#CCC(NC(=O)C1=CC=CC(C2CCOC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 17, 28, 28, 66, 66, 66, 66, 66, 17, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 1] 201 rigid atoms, others: [6, 39, 8, 9, 10, 11, 12, 13, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 310 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919813 none CC#CCC(NC(=O)C1=CC=CC(C2CCOC2)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 62, 18, 18, 6, 18, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 62, 98, 98, 201, 201, 201, 201, 201, 62, 18, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39]) total number of confs: 939 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919813 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919813 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919813/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919813 Building REAL300004919814 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919814' /scratch/stefan/7775247/working/building/REAL300004919814 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919814 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919814/0 /scratch/stefan/7775247/working/building/REAL300004919814 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 819) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/819 `/scratch/stefan/7775247/working/3D/819' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(S(C)(=O)=O)=CC(C)=C1C)C(=O)[O-]) `REAL300004919814.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919814 none CC#CCC(NC(=O)C1=CC(S(C)(=O)=O)=CC(C)=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 14, 5, 11, 11, 1, 1, 5, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 38, 10, 10, 1, 10, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 38, 53, 53, 91, 91, 91, 91, 91, 38, 10, 1, 3, 3, 3, 1, 2, 2, 2, 2, 2, 2] 166 rigid atoms, others: [34, 6, 8, 9, 10, 11, 15, 16, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 426 number of broken/clashed sets: 165 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919814 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919814 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919814/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919814 Building REAL300004919815 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919815' /scratch/stefan/7775247/working/building/REAL300004919815 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919815 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919815/0 /scratch/stefan/7775247/working/building/REAL300004919815 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/820 `/scratch/stefan/7775247/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)C2=CC=C(F)C=C2S1)C(=O)[O-]) `REAL300004919815.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919815 none CC#CCC(NC(=O)C1=C(C)C2=CC=C(F)C=C2S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 1, 1, 1, 1, 15, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 34, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 42, 42, 63, 63, 63, 63, 63, 34, 10, 2, 2, 2, 1, 1, 1] 63 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 281 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919815 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919815 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919815/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919815 Building REAL300004919816 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919816' /scratch/stefan/7775247/working/building/REAL300004919816 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919816 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919816/0 /scratch/stefan/7775247/working/building/REAL300004919816 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 821) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/821 `/scratch/stefan/7775247/working/3D/821' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)NC(C)C)=C1)C(=O)[O-]) `REAL300004919816.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919816 none CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)NC(C)C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 15, 15, 1, 17, 30, 30, 56, 56, 56, 56, 56, 17, 5, 1, 1, 1, 9, 15, 15, 15, 15, 15, 15, 15, 1] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 20, 42, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 328 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919816 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919816 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919816/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919816 Building REAL300004919817 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919817' /scratch/stefan/7775247/working/building/REAL300004919817 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004919817 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919817/0 /scratch/stefan/7775247/working/building/REAL300004919817 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/822 `/scratch/stefan/7775247/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)NC2=CC=CC=C2)C=C1)C(=O)[O-]) `REAL300004919817.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919817 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)NC2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 3, 3, 3, 9, 17, 17, 17, 17, 17, 1, 1, 9, 16, 16, 37, 37, 37, 37, 37, 9, 3, 1, 1, 9, 17, 17, 17, 17, 17, 1, 1] 201 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 43, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919817 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)NC2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 100, 33, 33, 9, 33, 9, 17, 17, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 1, 17, 17, 100, 131, 131, 201, 201, 201, 201, 201, 100, 33, 17, 17, 4, 1, 1, 1, 1, 1, 17, 17] 201 rigid atoms, others: [37, 38, 39, 40, 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, 42, 43]) total number of confs: 1062 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919817 /scratch/stefan/7775247/working /scratch/stefan/7775247 mkdir: created directory `1' /scratch/stefan/7775247/working/building/REAL300004919817/1 /scratch/stefan/7775247/working/building/REAL300004919817 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 1 (index: 823) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/823 `/scratch/stefan/7775247/working/3D/823' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=CC=C2)C=C1)C(=O)[O-]) `REAL300004919817.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004919817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919817 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 17, 1, 1, 9, 14, 14, 34, 34, 34, 34, 34, 9, 3, 1, 1, 17, 17, 17, 17, 17, 1, 1] 201 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 41, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919817 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)[N-]C2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 95, 33, 33, 17, 33, 9, 17, 17, 9, 4, 9, 9, 1, 1, 1, 1, 1, 1, 1, 17, 17, 95, 127, 127, 201, 201, 201, 201, 201, 95, 33, 17, 17, 1, 1, 1, 1, 1, 17, 17] 201 rigid atoms, others: [36, 37, 38, 39, 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, 41, 42]) total number of confs: 1069 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919817 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919817 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 1: /scratch/stefan/7775247/working/building/REAL300004919817/1.* 0: /scratch/stefan/7775247/working/building/REAL300004919817/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919817 Building REAL300004919818 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919818' /scratch/stefan/7775247/working/building/REAL300004919818 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919818 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919818/0 /scratch/stefan/7775247/working/building/REAL300004919818 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/824 `/scratch/stefan/7775247/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C)=C(C2=CC=CC(Cl)=C2)S1)C(=O)[O-]) `REAL300004919818.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919818 none CC#CCC(NC(=O)C1=CC(C)=C(C2=CC=CC(Cl)=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 16, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 39, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 7, 7, 2, 7, 7, 7, 1, 39, 61, 61, 91, 91, 91, 91, 91, 39, 13, 1, 2, 2, 2, 7, 7, 6, 7] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 476 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919818 none CC#CCC(NC(=O)C1=CC(C)=C(C2=CC=CC(Cl)=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 16, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 129, 64, 64, 7, 64, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 129, 156, 156, 201, 201, 201, 201, 201, 129, 64, 7, 7, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 908 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919818 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919818 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919818/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919818 Building REAL300004919819 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919819' /scratch/stefan/7775247/working/building/REAL300004919819 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919819 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919819/0 /scratch/stefan/7775247/working/building/REAL300004919819 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 825) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/825 `/scratch/stefan/7775247/working/3D/825' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)[C@@H](C)C1=CC2=CC=C(OC)C=C2C=C1)C(=O)[O-]) `REAL300004919819.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919819 none CC#CCC(NC(=O)[C@@H](C)C1=CC2=CC=C(OC)C=C2C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [156, 156, 156, 71, 33, 33, 8, 33, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 71, 115, 115, 156, 156, 156, 156, 156, 71, 33, 9, 9, 9, 1, 1, 1, 3, 3, 3, 1, 1, 1] 201 rigid atoms, others: [43, 36, 37, 38, 8, 44, 42, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41]) total number of confs: 850 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919819 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919819 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919819/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919819 Building REAL300004919820 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919820' /scratch/stefan/7775247/working/building/REAL300004919820 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919820 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919820/0 /scratch/stefan/7775247/working/building/REAL300004919820 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/826 `/scratch/stefan/7775247/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CSC(C(F)(F)F)=N1)C(=O)[O-]) `REAL300004919820.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919820 none CC#CCC(NC(=O)C1=CSC(C(F)(F)F)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 5, 15, 15, 15, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 34, 12, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 2, 1, 34, 43, 43, 63, 63, 63, 63, 63, 34, 13, 1] 63 rigid atoms, others: [6, 8, 9, 10, 11, 12, 16, 27] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919820 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919820 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919820/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919820 Building REAL300004919821 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919821' /scratch/stefan/7775247/working/building/REAL300004919821 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919821 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919821/0 /scratch/stefan/7775247/working/building/REAL300004919821 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 827) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/827 `/scratch/stefan/7775247/working/3D/827' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CSC2=CC(C)=CC=C12)C(=O)[O-]) `REAL300004919821.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919821 none CC#CCC(NC(=O)C1=CSC2=CC(C)=CC=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 1, 1, 5, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [102, 102, 102, 49, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 63, 63, 102, 102, 102, 102, 102, 49, 11, 1, 1, 2, 2, 2, 1, 1] 102 rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 32, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 460 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919821 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919821 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919821/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919821 Building REAL300004919822 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919822' /scratch/stefan/7775247/working/building/REAL300004919822 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919822 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919822/0 /scratch/stefan/7775247/working/building/REAL300004919822 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/828 `/scratch/stefan/7775247/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN=C(C(F)(F)F)N=C1)C(=O)[O-]) `REAL300004919822.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919822 none CC#CCC(NC(=O)C1=CN=C(C(F)(F)F)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 15, 15, 15, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 19, 27, 27, 46, 46, 46, 46, 46, 19, 7, 1, 1] 46 rigid atoms, others: [6, 8, 9, 10, 11, 12, 16, 17, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919822 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919822 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919822/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919822 Building REAL300004919823 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919823' /scratch/stefan/7775247/working/building/REAL300004919823 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919823 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919823/0 /scratch/stefan/7775247/working/building/REAL300004919823 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 829) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/829 `/scratch/stefan/7775247/working/3D/829' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C(F)(F)F)SC=N1)C(=O)[O-]) `REAL300004919823.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919823 none CC#CCC(NC(=O)C1=C(C(F)(F)F)SC=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'C.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 15, 15, 15, 14, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 25, 8, 8, 1, 8, 1, 1, 1, 2, 2, 2, 1, 1, 1, 25, 35, 35, 60, 60, 60, 60, 60, 25, 8, 1] 60 rigid atoms, others: [6, 8, 9, 10, 14, 15, 16, 27] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 276 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919823 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919823 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919823/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919823 Building REAL300004919824 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919824' /scratch/stefan/7775247/working/building/REAL300004919824 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919824 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919824/0 /scratch/stefan/7775247/working/building/REAL300004919824 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/830 `/scratch/stefan/7775247/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CNC2=CC=C(Cl)C=C12)C(=O)[O-]) `REAL300004919824.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919824 none CC#CCC(NC(=O)CC1=CNC2=CC=C(Cl)C=C12)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 8, 1, 1, 1, 1, 16, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 96, 49, 49, 8, 49, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 96, 142, 142, 201, 201, 201, 201, 201, 96, 49, 8, 8, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 1010 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919824 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919824 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919824/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919824 Building REAL300004919825 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919825' /scratch/stefan/7775247/working/building/REAL300004919825 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919825 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919825/0 /scratch/stefan/7775247/working/building/REAL300004919825 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 831) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/831 `/scratch/stefan/7775247/working/3D/831' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)CC1=CC=CC=C1Cl)C(=O)[O-]) `REAL300004919825.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919825 none CC#CCC(NC(=O)C(C)CC1=CC=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 112, 54, 54, 10, 54, 5, 10, 1, 1, 1, 1, 1, 1, 1, 1, 112, 145, 145, 201, 201, 201, 201, 201, 112, 54, 10, 10, 10, 10, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 947 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919825 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919825 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919825/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919825 Building REAL300004919826 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919826' /scratch/stefan/7775247/working/building/REAL300004919826 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919826 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919826/0 /scratch/stefan/7775247/working/building/REAL300004919826 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/832 `/scratch/stefan/7775247/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(CC2=CC=CC=C2F)CC1)C(=O)[O-]) `REAL300004919826.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919826 none CC#CCC(NC(=O)C1(CC2=CC=CC=C2F)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 15, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 25, 7, 7, 1, 7, 1, 1, 7, 16, 16, 7, 16, 16, 16, 1, 1, 25, 41, 41, 77, 77, 77, 77, 77, 25, 7, 7, 7, 16, 16, 16, 16, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 6, 8, 9, 17, 18, 38] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 426 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: REAL300004919826 none CC#CCC(NC(=O)C1(CC2=CC=CC=C2F)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 15, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 104, 41, 41, 16, 41, 5, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 104, 134, 134, 201, 201, 201, 201, 201, 104, 41, 5, 5, 1, 1, 1, 1, 16, 16, 16, 16] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 973 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919826 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919826 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919826/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919826 Building REAL300004919827 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919827' /scratch/stefan/7775247/working/building/REAL300004919827 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919827 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919827/0 /scratch/stefan/7775247/working/building/REAL300004919827 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 833) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/833 `/scratch/stefan/7775247/working/3D/833' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC=CC(OC)=C1F)C(=O)[O-]) `REAL300004919827.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919827 none CC#CCC(NC(=O)CCC1=CC=CC(OC)=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 12, 5, 1, 15, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 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: [112, 112, 112, 62, 27, 27, 8, 27, 6, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 63, 76, 76, 112, 112, 112, 112, 112, 63, 27, 8, 8, 6, 6, 1, 1, 1, 4, 4, 4] 131 rigid atoms, others: [33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 556 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919827 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919827 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919827/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919827 Building REAL300004919828 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919828' /scratch/stefan/7775247/working/building/REAL300004919828 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919828 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919828/0 /scratch/stefan/7775247/working/building/REAL300004919828 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/834 `/scratch/stefan/7775247/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C(C)C)C(Cl)=C1)C(=O)[O-]) `REAL300004919828.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919828 none CC#CCC(NC(=O)C1=CC=C(C(C)C)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 1, 16, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 28, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 38, 38, 67, 67, 67, 67, 67, 28, 7, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1] 67 rigid atoms, others: [37, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 310 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919828 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919828 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919828/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919828 Building REAL300004919829 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919829' /scratch/stefan/7775247/working/building/REAL300004919829 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919829 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919829/0 /scratch/stefan/7775247/working/building/REAL300004919829 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 835) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/835 `/scratch/stefan/7775247/working/3D/835' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)OC1=CC=CC2=CC=CC=C21)C(=O)[O-]) `REAL300004919829.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919829 none CC#CCC(NC(=O)C(C)OC1=CC=CC2=CC=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [115, 115, 115, 103, 61, 61, 17, 61, 7, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 103, 103, 103, 115, 115, 115, 115, 115, 103, 61, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1] 115 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 465 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919829 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919829 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919829/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919829 Building REAL300004919830 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919830' /scratch/stefan/7775247/working/building/REAL300004919830 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919830 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919830/0 /scratch/stefan/7775247/working/building/REAL300004919830 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/836 `/scratch/stefan/7775247/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Br)=C(OC)C(OC)=C1)C(=O)[O-]) `REAL300004919830.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919830 none CC#CCC(NC(=O)C1=CC(Br)=C(OC)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 17, 1, 12, 5, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 5, 1, 1, 3, 1, 26, 45, 45, 107, 107, 107, 107, 107, 26, 7, 1, 6, 6, 6, 4, 4, 4, 1] 201 rigid atoms, others: [36, 6, 8, 9, 10, 11, 12, 13, 15, 16, 18, 29] set([0, 1, 2, 3, 4, 5, 7, 14, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 492 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919830 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919830 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919830/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919830 Building REAL300004919831 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919831' /scratch/stefan/7775247/working/building/REAL300004919831 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919831 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919831/0 /scratch/stefan/7775247/working/building/REAL300004919831 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 837) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/837 `/scratch/stefan/7775247/working/3D/837' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCC1=CC=C(OC)C=C1OC)C(=O)[O-]) `REAL300004919831.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919831 none CC#CCC(NC(=O)CCCC1=CC=C(OC)C=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [169, 169, 169, 113, 68, 68, 18, 68, 9, 5, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 4, 113, 114, 114, 169, 169, 169, 169, 169, 113, 68, 18, 18, 9, 9, 5, 5, 1, 1, 3, 3, 3, 1, 4, 4, 4] 201 rigid atoms, others: [37, 38, 10, 11, 12, 13, 14, 15, 17, 18, 19, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 43, 44, 45]) total number of confs: 785 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919831 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919831 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919831/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919831 Building REAL300004919832 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919832' /scratch/stefan/7775247/working/building/REAL300004919832 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919832 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919832/0 /scratch/stefan/7775247/working/building/REAL300004919832 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/838 `/scratch/stefan/7775247/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CC=CC=C2OC(F)(F)F)O1)C(=O)[O-]) `REAL300004919832.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919832 none CC#CCC(NC(=O)C1=CC=C(C2=CC=CC=C2OC(F)(F)F)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 4, 4, 1, 4, 1, 1, 1, 1, 1, 12, 12, 3, 12, 12, 12, 44, 70, 70, 70, 1, 9, 12, 12, 20, 20, 20, 20, 20, 9, 4, 1, 1, 12, 12, 11, 12] 201 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 23] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 327 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919832 none CC#CCC(NC(=O)C1=CC=C(C2=CC=CC=C2OC(F)(F)F)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 56, 30, 30, 12, 30, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 14, 14, 14, 12, 56, 80, 80, 108, 108, 108, 108, 108, 56, 30, 12, 12, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 572 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919832 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919832 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919832/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919832 Building REAL300004919833 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919833' /scratch/stefan/7775247/working/building/REAL300004919833 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919833 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919833/0 /scratch/stefan/7775247/working/building/REAL300004919833 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 839) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/839 `/scratch/stefan/7775247/working/3D/839' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=C(OC)C=CC(F)=C2N1)C(=O)[O-]) `REAL300004919833.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919833 none CC#CCC(NC(=O)C1=CC2=C(OC)C=CC(F)=C2N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 15, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 2, 2, 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: [122, 122, 122, 43, 12, 12, 1, 12, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 43, 74, 74, 122, 122, 122, 122, 122, 43, 12, 1, 4, 4, 4, 1, 1, 1] 154 rigid atoms, others: [34, 35, 36, 6, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 32, 13, 33, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31]) total number of confs: 617 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919833 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919833 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919833/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919833 Building REAL300004919834 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919834' /scratch/stefan/7775247/working/building/REAL300004919834 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919834 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919834/0 /scratch/stefan/7775247/working/building/REAL300004919834 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/840 `/scratch/stefan/7775247/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CC=C(C(C)(C)C)C=C2)O1)C(=O)[O-]) `REAL300004919834.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919834 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(C(C)(C)C)C=C2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 30, 11, 10, 1, 10, 1, 1, 1, 1, 1, 7, 7, 1, 1, 9, 9, 9, 7, 7, 1, 30, 48, 48, 84, 84, 84, 84, 84, 30, 11, 1, 1, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7] 201 rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 12, 22] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 439 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919834 none CC#CCC(NC(=O)C1=CC=C(C2=CC=C(C(C)(C)C)C=C2)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [167, 167, 167, 83, 40, 40, 7, 40, 7, 7, 7, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 7, 83, 119, 119, 167, 167, 167, 167, 167, 83, 40, 7, 7, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1] 201 rigid atoms, others: [35, 36, 11, 12, 13, 14, 15, 16, 20, 21, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 830 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919834 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919834 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919834/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919834 Building REAL300004919835 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919835' /scratch/stefan/7775247/working/building/REAL300004919835 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919835 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919835/0 /scratch/stefan/7775247/working/building/REAL300004919835 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 841) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/841 `/scratch/stefan/7775247/working/3D/841' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CC)CC1=CC=C(C(F)(F)F)C=C1)C(=O)[O-]) `REAL300004919835.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919835 none CC#CCC(NC(=O)C(CC)CC1=CC=C(C(F)(F)F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 27, 16, 16, 5, 16, 1, 5, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 27, 27, 27, 38, 38, 38, 38, 38, 27, 16, 5, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1] 38 rigid atoms, others: [43, 38, 39, 8, 41, 42, 11, 12, 13, 14, 15, 16, 40, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919835 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919835 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919835/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919835 Building REAL300004919836 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919836' /scratch/stefan/7775247/working/building/REAL300004919836 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919836 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919836/0 /scratch/stefan/7775247/working/building/REAL300004919836 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/842 `/scratch/stefan/7775247/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC2=C(C=C1[N+](=O)[O-])OCCO2)C(=O)[O-]) `REAL300004919836.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919836 none CC#CCC(NC(=O)CC1=CC2=C(C=C1[N+](=O)[O-])OCCO2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 8, 11, 11, 12, 5, 5, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 128, 59, 28, 28, 4, 28, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 59, 86, 86, 128, 128, 128, 128, 128, 59, 28, 4, 4, 1, 1, 1, 1, 1, 1] 128 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 644 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919836 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919836 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919836/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919836 Building REAL300004919837 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919837' /scratch/stefan/7775247/working/building/REAL300004919837 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919837 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919837/0 /scratch/stefan/7775247/working/building/REAL300004919837 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 843) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/843 `/scratch/stefan/7775247/working/3D/843' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C)=NC(C(F)(F)F)=N1)C(=O)[O-]) `REAL300004919837.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919837 none CC#CCC(NC(=O)C1=CC(C)=NC(C(F)(F)F)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 5, 8, 1, 5, 15, 15, 15, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 28, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 28, 45, 45, 79, 79, 79, 79, 79, 28, 13, 1, 2, 2, 2] 79 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 18, 29] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 389 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919837 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919837 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919837/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919837 Building REAL300004919838 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919838' /scratch/stefan/7775247/working/building/REAL300004919838 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919838 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919838/0 /scratch/stefan/7775247/working/building/REAL300004919838 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/844 `/scratch/stefan/7775247/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=C(C)C(Br)=C1)C(=O)[O-]) `REAL300004919838.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919838 none CC#CCC(NC(=O)CC1=CC=C(C)C(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 5, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 68, 19, 19, 7, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 68, 112, 112, 201, 201, 201, 201, 201, 68, 19, 7, 7, 1, 1, 2, 2, 2, 1] 201 rigid atoms, others: [34, 8, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33]) total number of confs: 1001 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919838 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919838 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919838/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919838 Building REAL300004919839 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919839' /scratch/stefan/7775247/working/building/REAL300004919839 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919839 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919839/0 /scratch/stefan/7775247/working/building/REAL300004919839 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 845) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/845 `/scratch/stefan/7775247/working/3D/845' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CC)(CC)C1=CC=C(OC)C(OC)=C1)C(=O)[O-]) `REAL300004919839.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919839 none CC#CCC(NC(=O)C(CC)(CC)C1=CC=C(OC)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 33, 16, 16, 8, 16, 1, 8, 8, 8, 8, 1, 1, 1, 1, 1, 3, 1, 1, 3, 1, 33, 34, 34, 47, 47, 47, 47, 47, 33, 16, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 4, 4, 4, 3, 3, 3, 1] 69 rigid atoms, others: [51, 8, 43, 44, 13, 14, 15, 16, 17, 19, 20, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 18, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50]) total number of confs: 221 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919839 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919839 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919839/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919839 Building REAL300004919840 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919840' /scratch/stefan/7775247/working/building/REAL300004919840 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919840 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919840/0 /scratch/stefan/7775247/working/building/REAL300004919840 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/846 `/scratch/stefan/7775247/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(F)C=CC(OC)=C1OC)C(=O)[O-]) `REAL300004919840.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919840 none CC#CCC(NC(=O)C1=C(F)C=CC(OC)=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 15, 1, 1, 1, 12, 5, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 120, 120, 41, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 4, 1, 1, 7, 41, 67, 67, 120, 120, 120, 120, 120, 41, 13, 1, 1, 4, 4, 4, 7, 7, 7] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 16, 17, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 577 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919840 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919840 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919840/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919840 Building REAL300004919841 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919841' /scratch/stefan/7775247/working/building/REAL300004919841 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919841 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919841/0 /scratch/stefan/7775247/working/building/REAL300004919841 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 847) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/847 `/scratch/stefan/7775247/working/3D/847' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCC1=CC=CC(C(F)(F)F)=C1)C(=O)[O-]) `REAL300004919841.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919841 none CC#CCC(NC(=O)CCCC1=CC=CC(C(F)(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 91, 39, 39, 7, 39, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 91, 137, 137, 201, 201, 201, 201, 201, 91, 39, 7, 7, 3, 3, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 1026 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919841 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919841 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919841/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919841 Building REAL300004919842 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919842' /scratch/stefan/7775247/working/building/REAL300004919842 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919842 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919842/0 /scratch/stefan/7775247/working/building/REAL300004919842 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/848 `/scratch/stefan/7775247/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCC1=CC(F)=CC=C1F)C(=O)[O-]) `REAL300004919842.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919842 none CC#CCC(NC(=O)CCCC1=CC(F)=CC=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 5, 1, 1, 1, 15, 1, 1, 1, 15, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 103, 58, 58, 11, 58, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 103, 144, 144, 201, 201, 201, 201, 201, 103, 58, 11, 11, 5, 5, 5, 5, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 1014 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919842 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919842 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919842/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919842 Building REAL300004919843 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919843' /scratch/stefan/7775247/working/building/REAL300004919843 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919843 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919843/0 /scratch/stefan/7775247/working/building/REAL300004919843 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 849) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/849 `/scratch/stefan/7775247/working/3D/849' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1COC1CCOCC1)C(=O)[O-]) `REAL300004919843.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919843 none CC#CCC(NC(=O)C1=CC=CC=C1COC1CCOCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 5, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 24, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 5, 16, 32, 32, 32, 32, 32, 24, 39, 39, 55, 55, 55, 55, 55, 24, 9, 1, 1, 1, 1, 5, 5, 32, 32, 32, 32, 32, 32, 32, 32, 32] 201 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 7, 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]) total number of confs: 358 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919843 none CC#CCC(NC(=O)C1=CC=CC=C1COC1CCOCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 5, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 91, 91, 32, 91, 32, 32, 32, 32, 32, 13, 5, 1, 1, 1, 1, 1, 1, 1, 132, 162, 162, 201, 201, 201, 201, 201, 132, 91, 32, 32, 32, 32, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 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]) total number of confs: 909 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919843 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919843 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919843/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919843 Building REAL300004919844 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919844' /scratch/stefan/7775247/working/building/REAL300004919844 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919844 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919844/0 /scratch/stefan/7775247/working/building/REAL300004919844 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/850 `/scratch/stefan/7775247/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=C(C(F)(F)F)C=C2)CC1)C(=O)[O-]) `REAL300004919844.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919844 none CC#CCC(NC(=O)C1(C2=CC=C(C(F)(F)F)C=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [130, 130, 130, 54, 13, 13, 1, 13, 1, 1, 6, 6, 1, 1, 6, 6, 6, 6, 6, 1, 1, 54, 85, 85, 130, 130, 130, 130, 130, 54, 13, 6, 6, 6, 6, 1, 1, 1, 1] 181 rigid atoms, others: [35, 36, 37, 6, 8, 9, 19, 20, 38] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 653 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: REAL300004919844 none CC#CCC(NC(=O)C1(C2=CC=C(C(F)(F)F)C=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [181, 181, 181, 102, 38, 38, 6, 38, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 6, 6, 102, 130, 130, 181, 181, 181, 181, 181, 102, 38, 1, 1, 1, 1, 6, 6, 6, 6] 181 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 847 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919844 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919844 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919844/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919844 Building REAL300004919845 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919845' /scratch/stefan/7775247/working/building/REAL300004919845 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919845 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919845/0 /scratch/stefan/7775247/working/building/REAL300004919845 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 851) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/851 `/scratch/stefan/7775247/working/3D/851' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC)C=C1OCCC(C)C)C(=O)[O-]) `REAL300004919845.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919845 none CC#CCC(NC(=O)C1=CC=C(OC)C=C1OCCC(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 8, 8, 1, 8, 1, 1, 1, 1, 1, 2, 1, 1, 1, 9, 31, 45, 46, 46, 14, 23, 23, 37, 37, 37, 37, 37, 14, 8, 1, 1, 3, 3, 3, 1, 31, 31, 45, 45, 46, 46, 46, 46, 46, 46, 46] 201 rigid atoms, others: [32, 33, 37, 6, 8, 9, 10, 11, 12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 7, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 382 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919845 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919845 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919845/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919845 Building REAL300004919846 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919846' /scratch/stefan/7775247/working/building/REAL300004919846 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919846 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919846/0 /scratch/stefan/7775247/working/building/REAL300004919846 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/852 `/scratch/stefan/7775247/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=CC(OCCC)=C1)C(=O)[O-]) `REAL300004919846.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919846 none CC#CCC(NC(=O)CC1=CC=CC(OCCC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 26, 12, 12, 4, 12, 1, 1, 1, 1, 1, 1, 1, 6, 8, 18, 1, 26, 40, 40, 73, 73, 73, 73, 73, 26, 12, 4, 4, 1, 1, 1, 8, 8, 18, 18, 18, 18, 18, 1] 201 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 18, 41, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 415 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919846 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919846 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919846/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919846 Building REAL300004919847 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919847' /scratch/stefan/7775247/working/building/REAL300004919847 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919847 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919847/0 /scratch/stefan/7775247/working/building/REAL300004919847 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 853) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/853 `/scratch/stefan/7775247/working/3D/853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=CC(OCC(F)(F)F)=C1)C(=O)[O-]) `REAL300004919847.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919847 none CC#CCC(NC(=O)CC1=CC=CC(OCC(F)(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 42, 16, 16, 7, 16, 1, 1, 1, 1, 1, 1, 1, 6, 10, 10, 10, 10, 1, 42, 60, 60, 81, 81, 81, 81, 81, 42, 16, 7, 7, 1, 1, 1, 10, 10, 1] 201 rigid atoms, others: [33, 34, 35, 38, 8, 9, 10, 11, 12, 13, 14, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37]) total number of confs: 434 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919847 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919847 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919847/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919847 Building REAL300004919848 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919848' /scratch/stefan/7775247/working/building/REAL300004919848 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919848 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919848/0 /scratch/stefan/7775247/working/building/REAL300004919848 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/854 `/scratch/stefan/7775247/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC=C(CC(C)C)C=C1)C(=O)[O-]) `REAL300004919848.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919848 none CC#CCC(NC(=O)CCC1=CC=C(CC(C)C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 37, 17, 17, 4, 17, 2, 1, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1, 37, 57, 57, 85, 85, 85, 85, 85, 37, 17, 4, 4, 2, 2, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 1, 1] 201 rigid atoms, others: [34, 35, 9, 10, 11, 12, 13, 14, 45, 18, 19, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 469 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919848 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919848 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919848/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919848 Building REAL300004919849 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919849' /scratch/stefan/7775247/working/building/REAL300004919849 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919849 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919849/0 /scratch/stefan/7775247/working/building/REAL300004919849 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 855) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/855 `/scratch/stefan/7775247/working/3D/855' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC)C=C1OCC(C)C)C(=O)[O-]) `REAL300004919849.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919849 none CC#CCC(NC(=O)C1=CC=C(OC)C=C1OCC(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 22, 12, 12, 1, 12, 1, 1, 1, 1, 1, 2, 1, 1, 1, 9, 21, 30, 35, 22, 35, 35, 57, 57, 57, 57, 57, 22, 12, 1, 1, 2, 3, 3, 1, 21, 21, 35, 35, 35, 35, 35, 35, 35] 201 rigid atoms, others: [32, 36, 6, 8, 9, 10, 11, 12, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 464 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919849 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919849 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919849/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919849 Building REAL300004919850 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919850' /scratch/stefan/7775247/working/building/REAL300004919850 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919850 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919850/0 /scratch/stefan/7775247/working/building/REAL300004919850 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/856 `/scratch/stefan/7775247/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=CC=CC=C2N1CCC)C(=O)[O-]) `REAL300004919850.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919850 none CC#CCC(NC(=O)C1=CC2=CC=CC=C2N1CCC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 104, 41, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 41, 63, 63, 104, 104, 104, 104, 104, 41, 11, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 7] 201 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 516 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919850 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919850 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919850/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919850 Building REAL300004919851 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919851' /scratch/stefan/7775247/working/building/REAL300004919851 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919851 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919851/0 /scratch/stefan/7775247/working/building/REAL300004919851 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 857) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/857 `/scratch/stefan/7775247/working/3D/857' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(S(=O)(=O)N(C)C)=CN1C)C(=O)[O-]) `REAL300004919851.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919851 none CC#CCC(NC(=O)C1=CC(S(=O)(=O)N(C)C)=CN1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 14, 11, 11, 8, 5, 5, 1, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 25, 10, 10, 1, 10, 1, 1, 1, 1, 8, 8, 8, 21, 21, 1, 1, 1, 25, 39, 39, 57, 57, 57, 57, 57, 25, 10, 1, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2] 201 rigid atoms, others: [37, 6, 8, 9, 10, 11, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 359 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919851 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919851 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919851/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919851 Building REAL300004919852 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919852' /scratch/stefan/7775247/working/building/REAL300004919852 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919852 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919852/0 /scratch/stefan/7775247/working/building/REAL300004919852 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/858 `/scratch/stefan/7775247/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=CC=CC=C2C=C1OC(F)F)C(=O)[O-]) `REAL300004919852.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919852 none CC#CCC(NC(=O)C1=CC2=CC=CC=C2C=C1OC(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 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, 4, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 4, 4, 4, 5, 5, 5, 5, 5, 4, 3, 1, 1, 1, 1, 1, 1, 5] 6 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 38, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919852 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919852 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919852/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919852 Building REAL300004919853 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919853' /scratch/stefan/7775247/working/building/REAL300004919853 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919853 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919853/0 /scratch/stefan/7775247/working/building/REAL300004919853 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 859) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/859 `/scratch/stefan/7775247/working/3D/859' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(OC)=C(C)C([N+](=O)[O-])=C1)C(=O)[O-]) `REAL300004919853.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919853 none CC#CCC(NC(=O)C1=CC(OC)=C(C)C([N+](=O)[O-])=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 12, 5, 1, 5, 1, 8, 11, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 29, 7, 7, 1, 7, 1, 1, 1, 1, 3, 1, 1, 1, 1, 2, 2, 1, 29, 48, 48, 103, 103, 103, 103, 103, 29, 7, 1, 4, 4, 4, 2, 2, 2, 1] 123 rigid atoms, others: [37, 6, 8, 9, 10, 11, 13, 14, 15, 16, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 12, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 473 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919853 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919853 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919853/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919853 Building REAL300004919854 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919854' /scratch/stefan/7775247/working/building/REAL300004919854 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919854 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919854/0 /scratch/stefan/7775247/working/building/REAL300004919854 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/860 `/scratch/stefan/7775247/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OC)C=C1OCCC)C(=O)[O-]) `REAL300004919854.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919854 none CC#CCC(NC(=O)C1=CC=C(OC)C=C1OCCC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 11, 11, 1, 11, 1, 1, 1, 1, 1, 2, 1, 1, 1, 8, 28, 47, 21, 34, 34, 50, 50, 50, 50, 50, 21, 11, 1, 1, 3, 3, 3, 1, 28, 28, 52, 52, 52, 52, 52] 201 rigid atoms, others: [35, 6, 8, 9, 10, 11, 12, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 497 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919854 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919854 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919854/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919854 Building REAL300004919855 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919855' /scratch/stefan/7775247/working/building/REAL300004919855 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919855 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919855/0 /scratch/stefan/7775247/working/building/REAL300004919855 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 861) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/861 `/scratch/stefan/7775247/working/3D/861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NOC(COC2=CC=CC=C2F)=C1)C(=O)[O-]) `REAL300004919855.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919855 none CC#CCC(NC(=O)C1=NOC(COC2=CC=CC=C2F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 12, 1, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 9, 60, 95, 95, 65, 95, 95, 95, 1, 5, 8, 8, 12, 12, 12, 12, 12, 5, 2, 9, 9, 95, 95, 72, 95, 1] 201 rigid atoms, others: [38, 6, 8, 9, 10, 11, 12, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919855 none CC#CCC(NC(=O)C1=NOC(COC2=CC=CC=C2F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 12, 1, 5, 12, 1, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 157, 100, 100, 95, 100, 95, 95, 95, 28, 9, 1, 1, 1, 1, 1, 1, 1, 1, 95, 157, 169, 169, 201, 201, 201, 201, 201, 157, 100, 28, 28, 1, 1, 1, 1, 95] 201 rigid atoms, others: [34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 818 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919855 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919855 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919855/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919855 Building REAL300004919856 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919856' /scratch/stefan/7775247/working/building/REAL300004919856 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919856 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919856/0 /scratch/stefan/7775247/working/building/REAL300004919856 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/862 `/scratch/stefan/7775247/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)CC1=CC=C(OC)C(OC)=C1)C(=O)[O-]) `REAL300004919856.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919856 none CC#CCC(NC(=O)C(C)CC1=CC=C(OC)C(OC)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 19, 12, 12, 6, 12, 3, 6, 1, 1, 1, 1, 1, 1, 3, 1, 1, 3, 1, 19, 19, 19, 28, 28, 28, 28, 28, 19, 12, 6, 6, 6, 6, 3, 3, 1, 1, 4, 4, 4, 4, 4, 4, 1] 40 rigid atoms, others: [45, 37, 38, 10, 11, 12, 13, 14, 15, 17, 18, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 151 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919856 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919856 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919856/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919856 Building REAL300004919857 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919857' /scratch/stefan/7775247/working/building/REAL300004919857 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919857 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919857/0 /scratch/stefan/7775247/working/building/REAL300004919857 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 863) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/863 `/scratch/stefan/7775247/working/3D/863' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)CCCC)C=C1)C(=O)[O-]) `REAL300004919857.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919857 none CC#CCC(NC(=O)C1=CC=C(S(=O)(=O)CCCC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 14, 11, 11, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 2, 2, 2, 16, 20, 25, 1, 1, 9, 15, 15, 30, 30, 30, 30, 30, 9, 3, 1, 1, 16, 16, 20, 20, 25, 25, 26, 26, 26, 1, 1] 201 rigid atoms, others: [32, 43, 6, 8, 9, 10, 11, 12, 19, 20, 42, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919857 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919857 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919857/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919857 Building REAL300004919858 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919858' /scratch/stefan/7775247/working/building/REAL300004919858 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919858 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919858/0 /scratch/stefan/7775247/working/building/REAL300004919858 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/864 `/scratch/stefan/7775247/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)(C)C1=CC=C(OC(F)(F)F)C=C1)C(=O)[O-]) `REAL300004919858.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919858 none CC#CCC(NC(=O)C(C)(C)C1=CC=C(OC(F)(F)F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 28, 12, 12, 6, 12, 1, 6, 6, 1, 1, 1, 1, 1, 12, 20, 20, 20, 1, 1, 28, 45, 45, 60, 60, 60, 60, 60, 28, 12, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 8, 41, 11, 12, 13, 14, 15, 40, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 372 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919858 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919858 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919858/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919858 Building REAL300004919859 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919859' /scratch/stefan/7775247/working/building/REAL300004919859 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919859 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919859/0 /scratch/stefan/7775247/working/building/REAL300004919859 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 865) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/865 `/scratch/stefan/7775247/working/3D/865' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC(C(F)(F)F)=CC=C2Cl)CC1)C(=O)[O-]) `REAL300004919859.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919859 none CC#CCC(NC(=O)C1(C2=CC(C(F)(F)F)=CC=C2Cl)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 16, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [123, 123, 123, 47, 13, 13, 1, 13, 1, 1, 5, 5, 5, 5, 5, 5, 2, 5, 5, 5, 1, 1, 47, 71, 71, 123, 123, 123, 123, 123, 47, 13, 5, 2, 5, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 6, 8, 9, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 594 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: REAL300004919859 none CC#CCC(NC(=O)C1(C2=CC(C(F)(F)F)=CC=C2Cl)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 16, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 92, 34, 34, 5, 34, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 5, 5, 92, 127, 127, 201, 201, 201, 201, 201, 92, 34, 1, 1, 1, 5, 5, 5, 5] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 961 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919859 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919859 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919859/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919859 Building REAL300004919860 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919860' /scratch/stefan/7775247/working/building/REAL300004919860 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919860 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919860/0 /scratch/stefan/7775247/working/building/REAL300004919860 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/866 `/scratch/stefan/7775247/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)(C)C1=CC=C(Cl)C=C1F)C(=O)[O-]) `REAL300004919860.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919860 none CC#CCC(NC(=O)C(C)(C)C1=CC=C(Cl)C=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 15, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 97, 42, 42, 9, 42, 1, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 97, 136, 136, 201, 201, 201, 201, 201, 97, 42, 9, 9, 9, 10, 10, 10, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 8, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 989 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919860 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919860 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919860/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919860 Building REAL300004919861 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919861' /scratch/stefan/7775247/working/building/REAL300004919861 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919861 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919861/0 /scratch/stefan/7775247/working/building/REAL300004919861 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 867) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/867 `/scratch/stefan/7775247/working/3D/867' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Cl)=C(Cl)C=C1OC)C(=O)[O-]) `REAL300004919861.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919861 none CC#CCC(NC(=O)C1=CC(Cl)=C(Cl)C=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 16, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 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: [119, 119, 119, 46, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 46, 73, 73, 119, 119, 119, 119, 119, 46, 12, 1, 1, 4, 4, 4] 139 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 32, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 587 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919861 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919861 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919861/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919861 Building REAL300004919862 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919862' /scratch/stefan/7775247/working/building/REAL300004919862 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919862 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919862/0 /scratch/stefan/7775247/working/building/REAL300004919862 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/868 `/scratch/stefan/7775247/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1OC1=CC=CC(C)=C1)C(=O)[O-]) `REAL300004919862.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919862 none CC#CCC(NC(=O)C1=CC=CC=C1OC1=CC=CC(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 22, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 21, 21, 8, 21, 21, 21, 22, 34, 34, 51, 51, 51, 51, 51, 22, 12, 1, 1, 1, 1, 21, 21, 8, 21, 21, 21, 21] 201 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919862 none CC#CCC(NC(=O)C1=CC=CC=C1OC1=CC=CC(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 115, 83, 83, 21, 83, 21, 21, 20, 21, 21, 8, 1, 1, 1, 1, 1, 1, 1, 1, 115, 154, 154, 201, 201, 201, 201, 201, 115, 83, 21, 20, 21, 21, 1, 1, 1, 2, 2, 2, 1] 201 rigid atoms, others: [36, 37, 38, 42, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41]) total number of confs: 964 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919862 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919862 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919862/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919862 Building REAL300004919863 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919863' /scratch/stefan/7775247/working/building/REAL300004919863 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919863 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919863/0 /scratch/stefan/7775247/working/building/REAL300004919863 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 869) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/869 `/scratch/stefan/7775247/working/3D/869' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1CCC(C(C)(C)CC)CC1)C(=O)[O-]) `REAL300004919863.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919863 none CC#CCC(NC(=O)CC1CCC(C(C)(C)CC)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 31, 20, 20, 5, 20, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 1, 1, 31, 48, 48, 72, 72, 72, 72, 72, 31, 20, 5, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 5, 5, 6, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 51, 8, 9, 10, 11, 12, 13, 50, 49, 18, 19, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 407 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919863 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919863 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919863/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919863 Building REAL300004919864 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919864' /scratch/stefan/7775247/working/building/REAL300004919864 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919864 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919864/0 /scratch/stefan/7775247/working/building/REAL300004919864 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/870 `/scratch/stefan/7775247/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(CC2=CC=C(OC(F)(F)F)C=C2)CC1)C(=O)[O-]) `REAL300004919864.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919864 none CC#CCC(NC(=O)C1(CC2=CC=C(OC(F)(F)F)C=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 3, 3, 1, 3, 1, 1, 7, 7, 7, 7, 7, 49, 67, 67, 67, 7, 7, 1, 1, 9, 16, 16, 31, 31, 31, 31, 31, 9, 3, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [6, 39, 8, 9, 42, 40, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) 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: REAL300004919864 none CC#CCC(NC(=O)C1(CC2=CC=C(OC(F)(F)F)C=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 20, 9, 9, 7, 9, 2, 1, 1, 1, 1, 1, 1, 12, 25, 24, 25, 1, 1, 7, 7, 20, 32, 32, 52, 52, 52, 52, 52, 20, 9, 2, 2, 1, 1, 1, 1, 7, 7, 7, 7] 201 rigid atoms, others: [35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42]) total number of confs: 328 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919864 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919864 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919864/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919864 Building REAL300004919865 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919865' /scratch/stefan/7775247/working/building/REAL300004919865 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919865 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919865/0 /scratch/stefan/7775247/working/building/REAL300004919865 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 871) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/871 `/scratch/stefan/7775247/working/3D/871' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(CC2=CC=CC=C2Cl)CC1)C(=O)[O-]) `REAL300004919865.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919865 none CC#CCC(NC(=O)C1(CC2=CC=CC=C2Cl)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 16, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 22, 7, 7, 1, 7, 1, 1, 9, 22, 22, 15, 22, 22, 22, 1, 1, 22, 35, 35, 68, 68, 68, 68, 68, 22, 7, 9, 9, 22, 22, 22, 22, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 6, 8, 9, 17, 18, 38] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 388 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: REAL300004919865 none CC#CCC(NC(=O)C1(CC2=CC=CC=C2Cl)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 16, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 103, 41, 41, 22, 41, 6, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 103, 137, 137, 201, 201, 201, 201, 201, 103, 41, 6, 6, 1, 1, 1, 1, 22, 22, 22, 22] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 983 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919865 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919865 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919865/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919865 Building REAL300004919866 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919866' /scratch/stefan/7775247/working/building/REAL300004919866 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919866 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919866/0 /scratch/stefan/7775247/working/building/REAL300004919866 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/872 `/scratch/stefan/7775247/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=CC=C1S(C)(=O)=O)C(=O)[O-]) `REAL300004919866.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919866 none CC#CCC(NC(=O)CC1=CC=CC=C1S(C)(=O)=O)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2] 3 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) total number of confs: 19 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919866 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919866 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919866/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919866 Building REAL300004919867 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919867' /scratch/stefan/7775247/working/building/REAL300004919867 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919867 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919867/0 /scratch/stefan/7775247/working/building/REAL300004919867 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 873) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/873 `/scratch/stefan/7775247/working/3D/873' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CC1C1=CC(OC)=CC=C1OC)C(=O)[O-]) `REAL300004919867.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919867 none CC#CCC(NC(=O)C1CC1C1=CC(OC)=CC=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 1, 1, 1, 12, 5, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 30, 12, 12, 1, 12, 1, 1, 1, 1, 6, 6, 6, 9, 6, 6, 6, 6, 10, 30, 47, 47, 82, 82, 82, 82, 82, 30, 12, 1, 1, 1, 1, 6, 9, 9, 9, 6, 6, 10, 10, 10] 201 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 5, 7, 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]) total number of confs: 409 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919867 none CC#CCC(NC(=O)C1CC1C1=CC(OC)=CC=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 1, 1, 1, 12, 5, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [152, 152, 152, 68, 34, 34, 6, 34, 6, 6, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 3, 68, 100, 100, 152, 152, 152, 152, 152, 68, 34, 6, 6, 6, 6, 1, 3, 3, 3, 1, 1, 4, 4, 4] 201 rigid atoms, others: [35, 39, 40, 10, 11, 12, 13, 14, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 41, 42, 43]) total number of confs: 753 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919867 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919867 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919867/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919867 Building REAL300004919868 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919868' /scratch/stefan/7775247/working/building/REAL300004919868 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919868 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919868/0 /scratch/stefan/7775247/working/building/REAL300004919868 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/874 `/scratch/stefan/7775247/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OCCC)C=C1OCCCC)C(=O)[O-]) `REAL300004919868.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919868 none CC#CCC(NC(=O)C1=CC=C(OCCC)C=C1OCCCC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 6, 6, 14, 1, 1, 1, 6, 15, 26, 29, 7, 9, 9, 16, 16, 16, 16, 16, 7, 4, 1, 1, 6, 6, 14, 14, 15, 15, 15, 1, 15, 15, 29, 29, 29, 29, 29, 29, 29] 201 rigid atoms, others: [33, 34, 6, 8, 9, 10, 11, 12, 16, 17, 18, 42] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919868 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919868 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919868/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919868 Building REAL300004919869 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919869' /scratch/stefan/7775247/working/building/REAL300004919869 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919869 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919869/0 /scratch/stefan/7775247/working/building/REAL300004919869 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 875) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/875 `/scratch/stefan/7775247/working/3D/875' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(CC2=CC=CC(F)=C2)CCC1)C(=O)[O-]) `REAL300004919869.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919869 none CC#CCC(NC(=O)C1(CC2=CC=CC(F)=C2)CCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [67, 67, 67, 19, 5, 5, 1, 5, 1, 1, 7, 12, 12, 12, 12, 12, 12, 1, 1, 1, 19, 34, 34, 67, 67, 67, 67, 67, 19, 5, 7, 7, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1] 189 rigid atoms, others: [36, 37, 6, 39, 8, 9, 17, 18, 19, 41, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 342 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: REAL300004919869 none CC#CCC(NC(=O)C1(CC2=CC=CC(F)=C2)CCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 96, 31, 31, 12, 31, 3, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 96, 131, 131, 189, 189, 189, 189, 189, 96, 31, 3, 3, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12] 189 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16] 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, 36, 37, 38, 39, 40, 41]) total number of confs: 929 number of broken/clashed sets: 85 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919869 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919869 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919869/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919869 Building REAL300004919870 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919870' /scratch/stefan/7775247/working/building/REAL300004919870 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919870 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919870/0 /scratch/stefan/7775247/working/building/REAL300004919870 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/876 `/scratch/stefan/7775247/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC=C1CCC(F)(F)F)C(=O)[O-]) `REAL300004919870.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919870 none CC#CCC(NC(=O)C1=CC=CC=C1CCC(F)(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 32, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 32, 51, 51, 99, 99, 99, 99, 99, 32, 9, 1, 1, 1, 1, 6, 6, 8, 8] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37]) total number of confs: 482 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919870 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919870 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919870/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919870 Building REAL300004919871 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919871' /scratch/stefan/7775247/working/building/REAL300004919871 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919871 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919871/0 /scratch/stefan/7775247/working/building/REAL300004919871 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 877) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/877 `/scratch/stefan/7775247/working/3D/877' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(F)C1=CC=C(C(F)(F)F)C=C1)C(=O)[O-]) `REAL300004919871.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919871 none CC#CCC(NC(=O)C(F)C1=CC=C(C(F)(F)F)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 15, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 113, 41, 41, 7, 41, 1, 7, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 113, 147, 147, 201, 201, 201, 201, 201, 113, 41, 7, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 8, 10, 11, 12, 13, 14, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 961 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919871 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919871 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919871/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919871 Building REAL300004919872 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919872' /scratch/stefan/7775247/working/building/REAL300004919872 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919872 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919872/0 /scratch/stefan/7775247/working/building/REAL300004919872 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/878 `/scratch/stefan/7775247/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(Br)C(OC(F)(F)F)=C1)C(=O)[O-]) `REAL300004919872.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919872 none CC#CCC(NC(=O)C1=CC=C(Br)C(OC(F)(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 17, 1, 12, 5, 15, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 8, 20, 20, 20, 1, 16, 29, 29, 64, 64, 64, 64, 64, 16, 5, 1, 1, 1] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 14, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 350 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919872 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919872 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919872/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919872 Building REAL300004919873 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919873' /scratch/stefan/7775247/working/building/REAL300004919873 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919873 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919873/0 /scratch/stefan/7775247/working/building/REAL300004919873 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 879) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/879 `/scratch/stefan/7775247/working/3D/879' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C(C)C)C([N+](=O)[O-])=C1)C(=O)[O-]) `REAL300004919873.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919873 none CC#CCC(NC(=O)C1=CC=C(C(C)C)C([N+](=O)[O-])=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 1, 8, 11, 11, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2, 1, 25, 39, 39, 70, 70, 70, 70, 70, 25, 7, 1, 1, 2, 2, 2, 2, 2, 2, 2, 1] 70 rigid atoms, others: [6, 39, 8, 9, 10, 11, 12, 15, 16, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919873 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919873 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919873/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919873 Building REAL300004919874 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919874' /scratch/stefan/7775247/working/building/REAL300004919874 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919874 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919874/0 /scratch/stefan/7775247/working/building/REAL300004919874 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/880 `/scratch/stefan/7775247/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(C)(C)COCC1=CC=CC=C1)C(=O)[O-]) `REAL300004919874.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919874 none CC#CCC(NC(=O)C(C)(C)COCC1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 101, 101, 89, 101, 36, 89, 89, 16, 4, 1, 1, 1, 1, 1, 1, 1, 156, 173, 173, 201, 201, 201, 201, 201, 156, 101, 89, 89, 89, 89, 89, 89, 36, 36, 4, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 1023 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919874 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919874 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919874/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919874 Building REAL300004919875 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919875' /scratch/stefan/7775247/working/building/REAL300004919875 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919875 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919875/0 /scratch/stefan/7775247/working/building/REAL300004919875 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 881) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/881 `/scratch/stefan/7775247/working/3D/881' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C2=CC=CC=C2)OC(C)=C1C)C(=O)[O-]) `REAL300004919875.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919875 none CC#CCC(NC(=O)C1=C(C2=CC=CC=C2)OC(C)=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 5, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [157, 157, 157, 56, 12, 12, 1, 12, 1, 1, 1, 6, 6, 1, 6, 6, 1, 1, 1, 1, 1, 56, 87, 87, 157, 157, 157, 157, 157, 56, 12, 6, 6, 1, 6, 6, 2, 2, 2, 2, 2, 2] 185 rigid atoms, others: [6, 8, 9, 10, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 756 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919875 none CC#CCC(NC(=O)C1=C(C2=CC=CC=C2)OC(C)=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 5, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [185, 185, 185, 106, 37, 37, 6, 37, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 106, 136, 136, 185, 185, 185, 185, 185, 106, 37, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7] 185 rigid atoms, others: [32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 31] 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, 36, 37, 38, 39, 40, 41]) total number of confs: 861 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919875 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919875 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919875/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919875 Building REAL300004919876 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919876' /scratch/stefan/7775247/working/building/REAL300004919876 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919876 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919876/0 /scratch/stefan/7775247/working/building/REAL300004919876 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/882 `/scratch/stefan/7775247/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C)=C(Br)C(Cl)=C1)C(=O)[O-]) `REAL300004919876.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919876 none CC#CCC(NC(=O)C1=CC(C)=C(Br)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 5, 1, 17, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 38, 38, 70, 70, 70, 70, 70, 25, 7, 1, 2, 2, 2, 1] 70 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 31] set([0, 1, 2, 3, 4, 5, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30]) total number of confs: 334 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919876 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919876 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919876/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919876 Building REAL300004919877 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919877' /scratch/stefan/7775247/working/building/REAL300004919877 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919877 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919877/0 /scratch/stefan/7775247/working/building/REAL300004919877 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 883) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/883 `/scratch/stefan/7775247/working/3D/883' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1COC2=CC(C)=C(C)C=C21)C(=O)[O-]) `REAL300004919877.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919877 none CC#CCC(NC(=O)C1COC2=CC(C)=C(C)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 5, 12, 1, 1, 1, 5, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 44, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 60, 60, 95, 95, 95, 95, 95, 44, 13, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1] 95 rigid atoms, others: [32, 6, 39, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38]) total number of confs: 445 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919877 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919877 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919877/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919877 Building REAL300004919878 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919878' /scratch/stefan/7775247/working/building/REAL300004919878 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919878 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919878/0 /scratch/stefan/7775247/working/building/REAL300004919878 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/884 `/scratch/stefan/7775247/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)N(C)C(C)C)=C1)C(=O)[O-]) `REAL300004919878.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919878 none CC#CCC(NC(=O)C1=CC=CC(S(=O)(=O)N(C)C(C)C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 16, 16, 16, 16, 1, 16, 24, 24, 40, 40, 40, 40, 40, 16, 5, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1] 201 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 45, 21] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919878 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919878 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919878/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919878 Building REAL300004919879 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919879' /scratch/stefan/7775247/working/building/REAL300004919879 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919879 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919879/0 /scratch/stefan/7775247/working/building/REAL300004919879 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 885) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/885 `/scratch/stefan/7775247/working/3D/885' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C2=CC=C(OC)C=C2)=C(C)S1)C(=O)[O-]) `REAL300004919879.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919879 none CC#CCC(NC(=O)C1=CC(C2=CC=C(OC)C=C2)=C(C)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 5, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 119, 40, 12, 12, 1, 12, 1, 1, 1, 1, 4, 4, 2, 2, 7, 4, 4, 1, 1, 1, 40, 62, 62, 119, 119, 119, 119, 119, 40, 12, 1, 4, 4, 7, 7, 7, 4, 4, 2, 2, 2] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919879 none CC#CCC(NC(=O)C1=CC(C2=CC=C(OC)C=C2)=C(C)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 5, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [185, 185, 185, 83, 35, 35, 4, 35, 4, 4, 1, 1, 1, 1, 1, 1, 2, 1, 1, 4, 4, 4, 83, 116, 116, 185, 185, 185, 185, 185, 83, 35, 4, 1, 1, 3, 3, 3, 1, 1, 4, 4, 4] 201 rigid atoms, others: [33, 34, 38, 39, 10, 11, 12, 13, 14, 15, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 40, 41, 42]) total number of confs: 894 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919879 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919879 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919879/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919879 Building REAL300004919880 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919880' /scratch/stefan/7775247/working/building/REAL300004919880 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919880 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919880/0 /scratch/stefan/7775247/working/building/REAL300004919880 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/886 `/scratch/stefan/7775247/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CN1C2=CC=CC=C2N=C1C(F)(F)F)C(=O)[O-]) `REAL300004919880.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919880 none CC#CCC(NC(=O)CN1C2=CC=CC=C2N=C1C(F)(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 98, 32, 32, 5, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 98, 135, 135, 191, 191, 191, 191, 191, 98, 31, 4, 4, 1, 1, 1, 1] 191 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 933 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919880 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919880 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919880/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919880 Building REAL300004919881 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919881' /scratch/stefan/7775247/working/building/REAL300004919881 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919881 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919881/0 /scratch/stefan/7775247/working/building/REAL300004919881 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 887) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/887 `/scratch/stefan/7775247/working/3D/887' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N=C(C2=CC=C(Cl)C=C2)S1)C(=O)[O-]) `REAL300004919881.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919881 none CC#CCC(NC(=O)C1=C(C)N=C(C2=CC=C(Cl)C=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 16, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 38, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 3, 3, 2, 2, 3, 3, 1, 38, 56, 56, 76, 76, 76, 76, 76, 38, 11, 2, 2, 2, 3, 3, 3, 3] 80 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 20] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 383 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: REAL300004919881 none CC#CCC(NC(=O)C1=C(C)N=C(C2=CC=C(Cl)C=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 1, 16, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 53, 27, 27, 3, 27, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 53, 63, 63, 80, 80, 80, 80, 80, 53, 27, 4, 4, 4, 1, 1, 1, 1] 80 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 365 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919881 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919881 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919881/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919881 Building REAL300004919882 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919882' /scratch/stefan/7775247/working/building/REAL300004919882 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919882 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919882/0 /scratch/stefan/7775247/working/building/REAL300004919882 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/888 `/scratch/stefan/7775247/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N=C(COC2=CC=C(F)C=C2)S1)C(=O)[O-]) `REAL300004919882.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919882 none CC#CCC(NC(=O)C1=C(C)N=C(COC2=CC=C(F)C=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 5, 8, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 14, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 27, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 8, 19, 20, 20, 19, 20, 19, 19, 1, 27, 43, 43, 71, 71, 71, 71, 71, 27, 10, 2, 2, 2, 8, 8, 20, 20, 20, 20] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 22] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 390 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: REAL300004919882 none CC#CCC(NC(=O)C1=C(C)N=C(COC2=CC=C(F)C=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 5, 8, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 14, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 129, 66, 66, 19, 66, 19, 19, 20, 20, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 129, 160, 160, 201, 201, 201, 201, 201, 129, 66, 20, 20, 20, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 956 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919882 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919882 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919882/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919882 Building REAL300004919883 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919883' /scratch/stefan/7775247/working/building/REAL300004919883 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919883 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919883/0 /scratch/stefan/7775247/working/building/REAL300004919883 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 889) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/889 `/scratch/stefan/7775247/working/3D/889' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(OC)=C1[N+](=O)[O-])C(=O)[O-]) `REAL300004919883.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919883 none CC#CCC(NC(=O)C1=CC=CC(OC)=C1[N+](=O)[O-])C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 1, 8, 11, 11, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 2, 2, 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: [70, 70, 70, 22, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 3, 1, 1, 2, 2, 22, 36, 36, 70, 70, 70, 70, 70, 22, 7, 1, 1, 1, 4, 4, 4] 92 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 324 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919883 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919883 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919883/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919883 Building REAL300004919884 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919884' /scratch/stefan/7775247/working/building/REAL300004919884 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919884 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919884/0 /scratch/stefan/7775247/working/building/REAL300004919884 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/890 `/scratch/stefan/7775247/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(Br)C(C)=C1)C(=O)[O-]) `REAL300004919884.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919884 none CC#CCC(NC(=O)C1=CC=C(Br)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 17, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 30, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 30, 40, 40, 69, 69, 69, 69, 69, 30, 7, 1, 1, 2, 2, 2, 1] 69 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30]) total number of confs: 313 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919884 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919884 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919884/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919884 Building REAL300004919885 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919885' /scratch/stefan/7775247/working/building/REAL300004919885 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919885 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919885/0 /scratch/stefan/7775247/working/building/REAL300004919885 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 891) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/891 `/scratch/stefan/7775247/working/3D/891' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=CC(OC(F)(F)F)=C1)C(=O)[O-]) `REAL300004919885.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919885 none CC#CCC(NC(=O)CC1=CC=CC(OC(F)(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 23, 13, 13, 6, 13, 1, 1, 1, 1, 1, 1, 1, 13, 14, 14, 14, 1, 23, 34, 34, 55, 55, 55, 55, 55, 23, 13, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 283 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919885 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919885 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919885/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919885 Building REAL300004919886 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919886' /scratch/stefan/7775247/working/building/REAL300004919886 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919886 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919886/0 /scratch/stefan/7775247/working/building/REAL300004919886 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/892 `/scratch/stefan/7775247/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC(F)=CC=C1Br)C(=O)[O-]) `REAL300004919886.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919886 none CC#CCC(NC(=O)CC1=CC(F)=CC=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 15, 1, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 95, 38, 38, 6, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1, 95, 139, 139, 201, 201, 201, 201, 201, 95, 38, 6, 6, 1, 1, 1] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 995 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919886 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919886 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919886/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919886 Building REAL300004919887 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919887' /scratch/stefan/7775247/working/building/REAL300004919887 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919887 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919887/0 /scratch/stefan/7775247/working/building/REAL300004919887 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 893) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/893 `/scratch/stefan/7775247/working/3D/893' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1COC2=CC=C(OC)C=C2C1)C(=O)[O-]) `REAL300004919887.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919887 none CC#CCC(NC(=O)C1COC2=CC=C(OC)C=C2C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [135, 135, 135, 52, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 52, 84, 84, 135, 135, 135, 135, 135, 52, 13, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1] 171 rigid atoms, others: [32, 33, 34, 38, 6, 39, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 40, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 37, 35, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36]) total number of confs: 667 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919887 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919887 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919887/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919887 Building REAL300004919888 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919888' /scratch/stefan/7775247/working/building/REAL300004919888 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919888 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919888/0 /scratch/stefan/7775247/working/building/REAL300004919888 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/894 `/scratch/stefan/7775247/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Cl)=CC(C(F)(F)F)=C1)C(=O)[O-]) `REAL300004919888.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919888 none CC#CCC(NC(=O)C1=CC(Cl)=CC(C(F)(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 1, 5, 15, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 31, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 45, 45, 93, 93, 93, 93, 93, 31, 7, 1, 1, 1] 93 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 407 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919888 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919888 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919888/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919888 Building REAL300004919889 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919889' /scratch/stefan/7775247/working/building/REAL300004919889 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919889 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919889/0 /scratch/stefan/7775247/working/building/REAL300004919889 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 895) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/895 `/scratch/stefan/7775247/working/3D/895' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCN(S(=O)(=O)C2=CC=C(C)C=C2)C1)C(=O)[O-]) `REAL300004919889.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919889 none CC#CCC(NC(=O)C1CCCN(S(=O)(=O)C2=CC=C(C)C=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 22, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 19, 19, 19, 19, 19, 1, 22, 35, 35, 51, 51, 51, 51, 51, 22, 10, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 48, 40, 23, 49, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 294 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919889 none CC#CCC(NC(=O)C1CCCN(S(=O)(=O)C2=CC=C(C)C=C2)C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 87, 87, 19, 87, 19, 19, 19, 19, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 19, 140, 176, 176, 201, 201, 201, 201, 201, 140, 87, 19, 19, 19, 19, 19, 19, 19, 1, 1, 2, 2, 2, 1, 1, 19, 19] 201 rigid atoms, others: [41, 42, 13, 46, 47, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 48, 49]) total number of confs: 944 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919889 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919889 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919889/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919889 Building REAL300004919890 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919890' /scratch/stefan/7775247/working/building/REAL300004919890 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919890 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919890/0 /scratch/stefan/7775247/working/building/REAL300004919890 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/896 `/scratch/stefan/7775247/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(CC)CC1=CC=CC=C1C)C(=O)[O-]) `REAL300004919890.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919890 none CC#CCC(NC(=O)C(CC)CC1=CC=CC=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [187, 187, 187, 97, 44, 44, 11, 44, 6, 11, 16, 1, 1, 1, 1, 1, 1, 1, 1, 97, 132, 132, 187, 187, 187, 187, 187, 97, 44, 11, 16, 16, 16, 16, 16, 6, 6, 1, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [37, 38, 39, 40, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43]) total number of confs: 949 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919890 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919890 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919890/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919890 Building REAL300004919891 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919891' /scratch/stefan/7775247/working/building/REAL300004919891 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919891 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919891/0 /scratch/stefan/7775247/working/building/REAL300004919891 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 897) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/897 `/scratch/stefan/7775247/working/3D/897' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=CC(NC(C)=O)=C1)C(=O)[O-]) `REAL300004919891.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919891 none CC#CCC(NC(=O)CC1=CC=CC(NC(C)=O)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'C.3', 'O.2', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 1, 1, 1, 1, 1, 8, 1, 5, 11, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [144, 144, 144, 56, 17, 17, 7, 17, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 56, 84, 84, 144, 144, 144, 144, 144, 56, 17, 7, 7, 1, 1, 1, 4, 4, 4, 4, 1] 201 rigid atoms, others: [32, 33, 38, 8, 9, 10, 11, 12, 13, 14, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 708 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919891 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919891 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919891/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919891 Building REAL300004919892 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919892' /scratch/stefan/7775247/working/building/REAL300004919892 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919892 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919892/0 /scratch/stefan/7775247/working/building/REAL300004919892 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/898 `/scratch/stefan/7775247/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)OC(Br)=C1)C(=O)[O-]) `REAL300004919892.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919892 none CC#CCC(NC(=O)C1=C(C)OC(Br)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'Br', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 12, 1, 17, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 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: [74, 74, 74, 36, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 36, 53, 53, 74, 74, 74, 74, 74, 36, 12, 1, 1, 1, 1] 74 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 372 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919892 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919892 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919892/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919892 Building REAL300004919893 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919893' /scratch/stefan/7775247/working/building/REAL300004919893 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919893 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919893/0 /scratch/stefan/7775247/working/building/REAL300004919893 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 899) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/899 `/scratch/stefan/7775247/working/3D/899' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=C(Cl)C=C2Cl)CCCCC1)C(=O)[O-]) `REAL300004919893.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919893 none CC#CCC(NC(=O)C1(C2=CC=C(Cl)C=C2Cl)CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 22, 6, 6, 1, 6, 1, 1, 4, 4, 3, 3, 4, 4, 4, 1, 1, 1, 1, 1, 22, 32, 32, 51, 51, 51, 51, 51, 22, 6, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 58 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 41, 43, 44, 17, 18, 19, 20, 21, 40, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919893 none CC#CCC(NC(=O)C1(C2=CC=C(Cl)C=C2Cl)CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 16, 1, 1, 16, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 28, 10, 10, 4, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 28, 38, 38, 58, 58, 58, 58, 58, 28, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 58 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 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]) total number of confs: 274 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919893 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919893 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919893/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919893 Building REAL300004919894 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919894' /scratch/stefan/7775247/working/building/REAL300004919894 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919894 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919894/0 /scratch/stefan/7775247/working/building/REAL300004919894 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/900 `/scratch/stefan/7775247/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)[C@H]1C2CCC(CC2)[C@@H]1C(F)(F)F)C(=O)[O-]) `REAL300004919894.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919894 none CC#CCC(NC(=O)[C@H]1C2CCC(CC2)[C@@H]1C(F)(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [59, 59, 59, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 27, 39, 39, 59, 59, 59, 59, 59, 27, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 59 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 288 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919894 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919894 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919894/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919894 Building REAL300004919895 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919895' /scratch/stefan/7775247/working/building/REAL300004919895 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919895 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919895/0 /scratch/stefan/7775247/working/building/REAL300004919895 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 901) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/901 `/scratch/stefan/7775247/working/3D/901' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C2=CC=CC=C2)N(C2CCCC2)N=C1)C(=O)[O-]) `REAL300004919895.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919895 none CC#CCC(NC(=O)C1=C(C2=CC=CC=C2)N(C2CCCC2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 45, 13, 13, 1, 13, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 5, 5, 5, 5, 1, 1, 45, 69, 69, 108, 108, 108, 108, 108, 45, 13, 4, 4, 2, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1] 201 rigid atoms, others: [48, 6, 8, 9, 10, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 537 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919895 none CC#CCC(NC(=O)C1=C(C2=CC=CC=C2)N(C2CCCC2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 118, 56, 56, 5, 56, 5, 5, 5, 14, 14, 6, 14, 14, 1, 1, 1, 1, 1, 1, 5, 5, 118, 152, 152, 200, 200, 200, 200, 200, 118, 56, 14, 14, 9, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5] 201 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48]) total number of confs: 992 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919895 none CC#CCC(NC(=O)C1=C(C2=CC=CC=C2)N(C2CCCC2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [144, 144, 144, 76, 30, 30, 4, 30, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 14, 14, 14, 4, 4, 76, 102, 102, 144, 144, 144, 144, 144, 76, 30, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4] 201 rigid atoms, others: [34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 715 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919895 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919895 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919895/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919895 Building REAL300004919896 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919896' /scratch/stefan/7775247/working/building/REAL300004919896 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919896 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919896/0 /scratch/stefan/7775247/working/building/REAL300004919896 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/902 `/scratch/stefan/7775247/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(C)(=O)=O)S1)C(=O)[O-]) `REAL300004919896.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919896 none CC#CCC(NC(=O)C1=CC=C(S(C)(=O)=O)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'C.3', 'O.2', 'O.2', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 5, 11, 11, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 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: [110, 110, 110, 48, 12, 12, 1, 12, 1, 1, 1, 1, 1, 7, 7, 7, 1, 48, 73, 73, 110, 110, 110, 110, 110, 48, 12, 1, 1, 7, 7, 7] 169 rigid atoms, others: [6, 8, 9, 10, 11, 12, 16, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 557 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919896 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919896 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919896/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919896 Building REAL300004919897 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919897' /scratch/stefan/7775247/working/building/REAL300004919897 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919897 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919897/0 /scratch/stefan/7775247/working/building/REAL300004919897 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 903) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/903 `/scratch/stefan/7775247/working/3D/903' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC([N+](=O)[O-])=C(C)C=C1C)C(=O)[O-]) `REAL300004919897.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919897 none CC#CCC(NC(=O)C1=CC([N+](=O)[O-])=C(C)C=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 8, 11, 11, 1, 5, 1, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 34, 10, 10, 1, 10, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 34, 49, 49, 80, 80, 80, 80, 80, 34, 10, 1, 2, 2, 2, 1, 2, 2, 2] 80 rigid atoms, others: [33, 6, 8, 9, 10, 11, 14, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 34, 35, 36]) total number of confs: 385 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919897 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919897 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919897/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919897 Building REAL300004919898 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919898' /scratch/stefan/7775247/working/building/REAL300004919898 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919898 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919898/0 /scratch/stefan/7775247/working/building/REAL300004919898 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/904 `/scratch/stefan/7775247/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(N2C=CC=N2)C(C)=C1)C(=O)[O-]) `REAL300004919898.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919898 none CC#CCC(NC(=O)C1=CC=C(N2C=CC=N2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 1, 26, 43, 43, 82, 82, 82, 82, 82, 26, 7, 1, 1, 8, 8, 8, 2, 2, 2, 1] 155 rigid atoms, others: [38, 6, 8, 9, 10, 11, 12, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37]) total number of confs: 394 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919898 none CC#CCC(NC(=O)C1=CC=C(N2C=CC=N2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [155, 155, 155, 79, 35, 35, 8, 35, 7, 8, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 79, 100, 100, 155, 155, 155, 155, 155, 79, 35, 8, 8, 1, 1, 1, 8, 8, 8, 8] 155 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 715 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919898 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919898 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919898/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919898 Building REAL300004919899 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919899' /scratch/stefan/7775247/working/building/REAL300004919899 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919899 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919899/0 /scratch/stefan/7775247/working/building/REAL300004919899 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 905) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/905 `/scratch/stefan/7775247/working/3D/905' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OCC2=CC=NC=C2)C=C1)C(=O)[O-]) `REAL300004919899.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919899 none CC#CCC(NC(=O)C1=CC=C(OCC2=CC=NC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 4, 14, 33, 33, 14, 33, 33, 1, 1, 11, 19, 19, 40, 40, 40, 40, 40, 11, 4, 1, 1, 14, 14, 33, 33, 33, 33, 1, 1] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 40, 20, 21, 41] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 284 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: REAL300004919899 none CC#CCC(NC(=O)C1=CC=C(OCC2=CC=NC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 115, 65, 65, 33, 65, 15, 33, 33, 15, 5, 1, 1, 1, 1, 1, 1, 1, 33, 33, 115, 143, 143, 201, 201, 201, 201, 201, 115, 65, 33, 33, 5, 5, 1, 1, 1, 1, 33, 33] 201 rigid atoms, others: [36, 37, 38, 39, 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, 40, 41]) total number of confs: 1032 number of broken/clashed sets: 94 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919899 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919899 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919899/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919899 Building REAL300004919900 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919900' /scratch/stefan/7775247/working/building/REAL300004919900 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919900 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919900/0 /scratch/stefan/7775247/working/building/REAL300004919900 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/906 `/scratch/stefan/7775247/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=CC(F)=C2)C2=C1CCC2)C(=O)[O-]) `REAL300004919900.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919900 none CC#CCC(NC(=O)C1=NN(C2=CC=CC(F)=C2)C2=C1CCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 33, 11, 11, 1, 11, 1, 1, 1, 1, 11, 11, 10, 11, 11, 11, 1, 1, 1, 1, 1, 33, 48, 48, 77, 77, 77, 77, 77, 33, 11, 11, 11, 10, 11, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 6, 39, 8, 9, 10, 11, 40, 18, 19, 20, 21, 22, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 364 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919900 none CC#CCC(NC(=O)C1=NN(C2=CC=CC(F)=C2)C2=C1CCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 120, 53, 53, 11, 53, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 120, 150, 150, 201, 201, 201, 201, 201, 120, 53, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 933 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919900 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919900 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919900/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919900 Building REAL300004919901 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919901' /scratch/stefan/7775247/working/building/REAL300004919901 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919901 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919901/0 /scratch/stefan/7775247/working/building/REAL300004919901 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 907) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/907 `/scratch/stefan/7775247/working/3D/907' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=CC(F)=C2)C2=C1CCCC2)C(=O)[O-]) `REAL300004919901.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919901 none CC#CCC(NC(=O)C1=NN(C2=CC=CC(F)=C2)C2=C1CCCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 33, 11, 11, 1, 11, 1, 1, 1, 1, 7, 7, 5, 7, 7, 7, 1, 1, 1, 1, 1, 1, 33, 48, 48, 68, 68, 68, 68, 68, 33, 11, 7, 7, 6, 7, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 43, 38, 6, 39, 8, 9, 10, 11, 44, 45, 40, 18, 19, 20, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 339 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: REAL300004919901 none CC#CCC(NC(=O)C1=NN(C2=CC=CC(F)=C2)C2=C1CCCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 47, 47, 7, 47, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 116, 149, 149, 201, 201, 201, 201, 201, 116, 47, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] 201 rigid atoms, others: [34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 949 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919901 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919901 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919901/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919901 Building REAL300004919902 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919902' /scratch/stefan/7775247/working/building/REAL300004919902 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919902 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919902/0 /scratch/stefan/7775247/working/building/REAL300004919902 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/908 `/scratch/stefan/7775247/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC(C)=CC=C2F)C2=C1CCC2)C(=O)[O-]) `REAL300004919902.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919902 none CC#CCC(NC(=O)C1=NN(C2=CC(C)=CC=C2F)C2=C1CCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 5, 1, 1, 1, 15, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [80, 80, 80, 37, 11, 11, 1, 11, 1, 1, 1, 1, 10, 10, 10, 3, 10, 10, 10, 1, 1, 1, 1, 1, 37, 53, 53, 80, 80, 80, 80, 80, 37, 11, 10, 10, 10, 10, 8, 10, 1, 1, 1, 1, 1, 1] 182 rigid atoms, others: [41, 43, 6, 8, 9, 10, 11, 44, 45, 40, 19, 20, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 403 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919902 none CC#CCC(NC(=O)C1=NN(C2=CC(C)=CC=C2F)C2=C1CCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 5, 1, 1, 1, 15, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [182, 182, 182, 105, 42, 42, 10, 42, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 105, 132, 132, 182, 182, 182, 182, 182, 105, 42, 1, 2, 2, 2, 1, 1, 10, 10, 10, 10, 10, 10] 182 rigid atoms, others: [34, 38, 39, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 40, 41, 42, 43, 44, 45]) total number of confs: 857 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919902 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919902 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919902/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919902 Building REAL300004919903 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919903' /scratch/stefan/7775247/working/building/REAL300004919903 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919903 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919903/0 /scratch/stefan/7775247/working/building/REAL300004919903 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 909) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/909 `/scratch/stefan/7775247/working/3D/909' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=CC(F)=C2F)C2=C1CCC2)C(=O)[O-]) `REAL300004919903.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919903 none CC#CCC(NC(=O)C1=NN(C2=CC=CC(F)=C2F)C2=C1CCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 15, 1, 1, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 34, 11, 11, 1, 11, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 34, 47, 47, 72, 72, 72, 72, 72, 34, 11, 9, 9, 9, 1, 1, 1, 1, 1, 1] 161 rigid atoms, others: [41, 37, 6, 39, 8, 9, 10, 11, 40, 19, 20, 21, 22, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919903 none CC#CCC(NC(=O)C1=NN(C2=CC=CC(F)=C2F)C2=C1CCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 15, 1, 15, 1, 1, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [161, 161, 161, 94, 39, 39, 9, 39, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 94, 120, 120, 161, 161, 161, 161, 161, 94, 39, 1, 1, 1, 9, 9, 9, 9, 9, 9] 161 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 767 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919903 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919903 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919903/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919903 Building REAL300004919904 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919904' /scratch/stefan/7775247/working/building/REAL300004919904 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919904 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919904/0 /scratch/stefan/7775247/working/building/REAL300004919904 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/910 `/scratch/stefan/7775247/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=C(C)C=CC=C2F)C2=C1CCC2)C(=O)[O-]) `REAL300004919904.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919904 none CC#CCC(NC(=O)C1=NN(C2=C(C)C=CC=C2F)C2=C1CCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [82, 82, 82, 36, 11, 11, 1, 11, 1, 1, 1, 1, 7, 7, 7, 2, 7, 7, 7, 1, 1, 1, 1, 1, 36, 58, 58, 82, 82, 82, 82, 82, 36, 11, 7, 7, 7, 7, 5, 7, 1, 1, 1, 1, 1, 1] 174 rigid atoms, others: [41, 43, 6, 8, 9, 10, 11, 44, 45, 40, 19, 20, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 432 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919904 none CC#CCC(NC(=O)C1=NN(C2=C(C)C=CC=C2F)C2=C1CCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 8, 8, 1, 1, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [174, 174, 174, 102, 42, 42, 7, 42, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 102, 132, 132, 174, 174, 174, 174, 174, 102, 42, 2, 2, 2, 1, 1, 1, 7, 7, 7, 7, 7, 7] 174 rigid atoms, others: [37, 38, 39, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 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: 843 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919904 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919904 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919904/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919904 Building REAL300004919905 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919905' /scratch/stefan/7775247/working/building/REAL300004919905 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919905 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919905/0 /scratch/stefan/7775247/working/building/REAL300004919905 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 911) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/911 `/scratch/stefan/7775247/working/3D/911' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Br)=C(C)S1)C(=O)[O-]) `REAL300004919905.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919905 none CC#CCC(NC(=O)C1=CC(Br)=C(C)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.3', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 17, 1, 5, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 35, 11, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 35, 48, 48, 67, 67, 67, 67, 67, 35, 12, 1, 2, 2, 2] 67 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 25] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28]) total number of confs: 336 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919905 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919905 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919905/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919905 Building REAL300004919906 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919906' /scratch/stefan/7775247/working/building/REAL300004919906 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919906 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919906/0 /scratch/stefan/7775247/working/building/REAL300004919906 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/912 `/scratch/stefan/7775247/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=C(F)C=CC=C2F)CCC1)C(=O)[O-]) `REAL300004919906.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919906 none CC#CCC(NC(=O)C1(C2=C(F)C=CC=C2F)CCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 1, 1, 15, 1, 1, 1, 1, 15, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 44, 12, 12, 1, 12, 1, 1, 4, 4, 4, 2, 4, 4, 4, 1, 1, 1, 44, 58, 58, 91, 91, 91, 91, 91, 44, 12, 4, 3, 4, 1, 1, 1, 1, 1, 1] 96 rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 17, 18, 19, 38] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 415 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: REAL300004919906 none CC#CCC(NC(=O)C1(C2=C(F)C=CC=C2F)CCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 1, 1, 15, 1, 1, 1, 1, 15, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 48, 15, 15, 4, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 48, 62, 62, 96, 96, 96, 96, 96, 48, 15, 1, 1, 1, 4, 4, 4, 4, 4, 4] 96 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 427 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919906 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919906 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919906/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919906 Building REAL300004919907 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919907' /scratch/stefan/7775247/working/building/REAL300004919907 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919907 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919907/0 /scratch/stefan/7775247/working/building/REAL300004919907 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 913) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/913 `/scratch/stefan/7775247/working/3D/913' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=C(N2C=NN=C2)C=C1)C(=O)[O-]) `REAL300004919907.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919907 none CC#CCC(NC(=O)CC1=CC=C(N2C=NN=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [179, 179, 179, 52, 12, 12, 4, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 52, 85, 85, 179, 179, 179, 179, 179, 52, 12, 4, 4, 1, 1, 5, 5, 1, 1] 180 rigid atoms, others: [32, 33, 36, 37, 8, 9, 10, 11, 12, 13, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35]) total number of confs: 808 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919907 none CC#CCC(NC(=O)CC1=CC=C(N2C=NN=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 8, 8, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [174, 174, 174, 76, 26, 25, 7, 25, 1, 2, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 76, 105, 105, 174, 174, 174, 174, 174, 76, 26, 7, 7, 7, 7, 1, 1, 7, 7] 175 rigid atoms, others: [34, 35, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37]) total number of confs: 821 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919907 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919907 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919907/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919907 Building REAL300004919908 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919908' /scratch/stefan/7775247/working/building/REAL300004919908 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919908 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919908/0 /scratch/stefan/7775247/working/building/REAL300004919908 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/914 `/scratch/stefan/7775247/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC=CC(OC(F)F)=C1)C(=O)[O-]) `REAL300004919908.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919908 none CC#CCC(NC(=O)CCC1=CC=CC(OC(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 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: [31, 31, 31, 19, 13, 13, 6, 12, 2, 1, 1, 1, 1, 1, 1, 1, 13, 24, 24, 1, 19, 23, 23, 31, 31, 31, 31, 31, 19, 13, 6, 6, 2, 2, 1, 1, 1, 24, 1] 102 rigid atoms, others: [34, 35, 36, 38, 9, 10, 11, 12, 13, 14, 15, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919908 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919908 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919908/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919908 Building REAL300004919909 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919909' /scratch/stefan/7775247/working/building/REAL300004919909 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919909 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919909/0 /scratch/stefan/7775247/working/building/REAL300004919909 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 915) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/915 `/scratch/stefan/7775247/working/3D/915' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=COC(C2=C(F)C=CC=C2F)=N1)C(=O)[O-]) `REAL300004919909.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919909 none CC#CCC(NC(=O)C1=COC(C2=C(F)C=CC=C2F)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 1, 15, 1, 1, 1, 1, 15, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [90, 90, 90, 38, 12, 12, 1, 12, 1, 1, 1, 1, 1, 6, 7, 6, 1, 6, 6, 7, 1, 38, 57, 57, 90, 90, 90, 90, 90, 38, 12, 1, 7, 1, 7] 180 rigid atoms, others: [6, 8, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34]) total number of confs: 455 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919909 none CC#CCC(NC(=O)C1=COC(C2=C(F)C=CC=C2F)=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 1, 15, 1, 1, 1, 1, 15, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [178, 178, 178, 113, 58, 58, 7, 58, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 113, 137, 137, 178, 178, 178, 178, 178, 113, 58, 7, 1, 1, 1] 178 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 799 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919909 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919909 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919909/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919909 Building REAL300004919910 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919910' /scratch/stefan/7775247/working/building/REAL300004919910 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919910 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919910/0 /scratch/stefan/7775247/working/building/REAL300004919910 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/916 `/scratch/stefan/7775247/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=CC(Cl)=C2F)C2=C1CCC2)C(=O)[O-]) `REAL300004919910.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919910 none CC#CCC(NC(=O)C1=NN(C2=CC=CC(Cl)=C2F)C2=C1CCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 15, 1, 1, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 34, 11, 11, 1, 11, 1, 1, 1, 1, 9, 9, 8, 9, 9, 9, 9, 1, 1, 1, 1, 1, 34, 47, 47, 72, 72, 72, 72, 72, 34, 11, 9, 9, 9, 1, 1, 1, 1, 1, 1] 161 rigid atoms, others: [41, 37, 6, 39, 8, 9, 10, 11, 40, 19, 20, 21, 22, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 350 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919910 none CC#CCC(NC(=O)C1=NN(C2=CC=CC(Cl)=C2F)C2=C1CCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 16, 1, 15, 1, 1, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [161, 161, 161, 93, 39, 39, 9, 39, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 93, 119, 119, 161, 161, 161, 161, 161, 93, 39, 1, 1, 1, 9, 9, 9, 9, 9, 9] 161 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 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/7775247/working/building/REAL300004919910 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919910 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919910/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919910 Building REAL300004919911 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919911' /scratch/stefan/7775247/working/building/REAL300004919911 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919911 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919911/0 /scratch/stefan/7775247/working/building/REAL300004919911 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 917) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/917 `/scratch/stefan/7775247/working/3D/917' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC(C)=CC(F)=C2)C2=C1CCC2)C(=O)[O-]) `REAL300004919911.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919911 none CC#CCC(NC(=O)C1=NN(C2=CC(C)=CC(F)=C2)C2=C1CCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 5, 1, 1, 15, 1, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 26, 9, 9, 1, 9, 1, 1, 1, 1, 10, 10, 10, 9, 10, 10, 10, 1, 1, 1, 1, 1, 26, 43, 43, 69, 69, 69, 69, 69, 26, 9, 10, 10, 10, 10, 9, 10, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 43, 6, 8, 9, 10, 11, 44, 45, 40, 19, 20, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919911 none CC#CCC(NC(=O)C1=NN(C2=CC(C)=CC(F)=C2)C2=C1CCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 5, 1, 1, 15, 1, 1, 1, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 117, 52, 52, 10, 52, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 117, 156, 156, 201, 201, 201, 201, 201, 117, 52, 1, 2, 2, 2, 1, 1, 10, 10, 10, 10, 10, 10] 201 rigid atoms, others: [34, 38, 39, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 40, 41, 42, 43, 44, 45]) total number of confs: 992 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919911 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919911 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919911/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919911 Building REAL300004919912 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919912' /scratch/stefan/7775247/working/building/REAL300004919912 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919912 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919912/0 /scratch/stefan/7775247/working/building/REAL300004919912 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/918 `/scratch/stefan/7775247/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=CC=CC(Cl)=C2S1)C(=O)[O-]) `REAL300004919912.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919912 none CC#CCC(NC(=O)C1=CC2=CC=CC(Cl)=C2S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 16, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 39, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 51, 51, 73, 73, 73, 73, 73, 39, 12, 1, 1, 1, 1] 73 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 346 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919912 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919912 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919912/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919912 Building REAL300004919913 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919913' /scratch/stefan/7775247/working/building/REAL300004919913 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919913 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919913/0 /scratch/stefan/7775247/working/building/REAL300004919913 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 919) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/919 `/scratch/stefan/7775247/working/3D/919' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CN1N=NN=C1C1=CSC=C1)C(=O)[O-]) `REAL300004919913.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919913 none CC#CCC(NC(=O)CN1N=NN=C1C1=CSC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 8, 8, 8, 1, 1, 1, 14, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 113, 54, 25, 25, 6, 25, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 54, 80, 80, 113, 113, 113, 113, 113, 54, 25, 6, 6, 7, 7, 7] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919913 none CC#CCC(NC(=O)CN1N=NN=C1C1=CSC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 8, 8, 8, 1, 1, 1, 14, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 81, 81, 19, 81, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 131, 168, 168, 201, 201, 201, 201, 201, 131, 81, 19, 19, 1, 1, 1] 201 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 989 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919913 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919913 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919913/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919913 Building REAL300004919914 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919914' /scratch/stefan/7775247/working/building/REAL300004919914 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919914 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919914/0 /scratch/stefan/7775247/working/building/REAL300004919914 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/920 `/scratch/stefan/7775247/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)N(C2=CC=C(F)C(F)=C2)N=N1)C(=O)[O-]) `REAL300004919914.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919914 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=C(F)C(F)=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 15, 1, 15, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 31, 10, 10, 1, 10, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 1, 1, 31, 42, 42, 58, 58, 58, 58, 58, 31, 10, 2, 2, 2, 6, 6, 6] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 299 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: REAL300004919914 none CC#CCC(NC(=O)C1=C(C)N(C2=CC=C(F)C(F)=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 8, 1, 1, 1, 1, 15, 1, 15, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 117, 41, 41, 6, 41, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 117, 158, 158, 201, 201, 201, 201, 201, 117, 41, 6, 6, 6, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 1017 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919914 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919914 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919914/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919914 Building REAL300004919915 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919915' /scratch/stefan/7775247/working/building/REAL300004919915 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919915 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919915/0 /scratch/stefan/7775247/working/building/REAL300004919915 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 921) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/921 `/scratch/stefan/7775247/working/3D/921' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC(F)=CC(F)=C2)C2=C1CCC2)C(=O)[O-]) `REAL300004919915.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919915 none CC#CCC(NC(=O)C1=NN(C2=CC(F)=CC(F)=C2)C2=C1CCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 15, 1, 1, 15, 1, 1, 1, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 106, 106, 40, 11, 11, 1, 11, 1, 1, 1, 1, 6, 6, 6, 2, 6, 6, 6, 1, 1, 1, 1, 1, 40, 65, 65, 106, 106, 106, 106, 106, 40, 11, 6, 6, 6, 1, 1, 1, 1, 1, 1] 169 rigid atoms, others: [41, 37, 6, 39, 8, 9, 10, 11, 40, 19, 20, 21, 22, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 539 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919915 none CC#CCC(NC(=O)C1=NN(C2=CC(F)=CC(F)=C2)C2=C1CCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 15, 1, 1, 15, 1, 1, 1, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [169, 169, 169, 100, 43, 43, 8, 43, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 100, 127, 127, 169, 169, 169, 169, 169, 100, 43, 1, 1, 1, 8, 8, 8, 8, 8, 8] 169 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 801 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919915 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919915 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919915/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919915 Building REAL300004919916 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919916' /scratch/stefan/7775247/working/building/REAL300004919916 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919916 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919916/0 /scratch/stefan/7775247/working/building/REAL300004919916 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/922 `/scratch/stefan/7775247/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=C(Cl)C=C2F)C2=C1CCC2)C(=O)[O-]) `REAL300004919916.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919916 none CC#CCC(NC(=O)C1=NN(C2=CC=C(Cl)C=C2F)C2=C1CCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 15, 1, 1, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [75, 75, 75, 36, 12, 12, 1, 12, 1, 1, 1, 1, 10, 10, 2, 9, 10, 10, 10, 1, 1, 1, 1, 1, 36, 49, 49, 75, 75, 75, 75, 75, 36, 12, 10, 10, 10, 1, 1, 1, 1, 1, 1] 179 rigid atoms, others: [41, 37, 6, 39, 8, 9, 10, 11, 40, 19, 20, 21, 22, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 375 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919916 none CC#CCC(NC(=O)C1=NN(C2=CC=C(Cl)C=C2F)C2=C1CCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 15, 1, 1, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [179, 179, 179, 104, 47, 47, 10, 47, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 104, 134, 134, 179, 179, 179, 179, 179, 104, 47, 1, 1, 1, 10, 10, 10, 10, 10, 10] 179 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 846 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919916 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919916 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919916/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919916 Building REAL300004919917 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919917' /scratch/stefan/7775247/working/building/REAL300004919917 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919917 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919917/0 /scratch/stefan/7775247/working/building/REAL300004919917 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 923) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/923 `/scratch/stefan/7775247/working/3D/923' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC(Cl)=CC=C2F)C2=C1CCC2)C(=O)[O-]) `REAL300004919917.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919917 none CC#CCC(NC(=O)C1=NN(C2=CC(Cl)=CC=C2F)C2=C1CCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 16, 1, 1, 1, 15, 1, 1, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 36, 10, 10, 1, 10, 1, 1, 1, 1, 10, 10, 10, 3, 10, 10, 10, 1, 1, 1, 1, 1, 36, 52, 52, 87, 87, 87, 87, 87, 36, 10, 10, 3, 10, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 37, 6, 39, 8, 9, 10, 11, 40, 19, 20, 21, 22, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 423 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919917 none CC#CCC(NC(=O)C1=NN(C2=CC(Cl)=CC=C2F)C2=C1CCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 16, 1, 1, 1, 15, 1, 1, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 117, 45, 45, 10, 45, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 117, 146, 146, 201, 201, 201, 201, 201, 117, 45, 1, 1, 1, 10, 10, 10, 10, 10, 10] 201 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 956 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919917 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919917 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919917/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919917 Building REAL300004919918 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919918' /scratch/stefan/7775247/working/building/REAL300004919918 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919918 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919918/0 /scratch/stefan/7775247/working/building/REAL300004919918 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/924 `/scratch/stefan/7775247/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=C(Cl)C(F)=C2)C2=C1CCC2)C(=O)[O-]) `REAL300004919918.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919918 none CC#CCC(NC(=O)C1=NN(C2=CC=C(Cl)C(F)=C2)C2=C1CCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 16, 1, 15, 1, 1, 1, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 32, 11, 11, 1, 11, 1, 1, 1, 1, 11, 11, 10, 10, 11, 11, 11, 1, 1, 1, 1, 1, 32, 49, 49, 72, 72, 72, 72, 72, 32, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [41, 37, 6, 39, 8, 9, 10, 11, 40, 19, 20, 21, 22, 23, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 369 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919918 none CC#CCC(NC(=O)C1=NN(C2=CC=C(Cl)C(F)=C2)C2=C1CCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 16, 1, 15, 1, 1, 1, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 124, 52, 52, 11, 52, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 124, 151, 151, 201, 201, 201, 201, 201, 124, 52, 1, 1, 1, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) total number of confs: 925 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919918 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919918 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919918/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919918 Building REAL300004919919 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919919' /scratch/stefan/7775247/working/building/REAL300004919919 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919919 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919919/0 /scratch/stefan/7775247/working/building/REAL300004919919 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 925) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/925 `/scratch/stefan/7775247/working/3D/925' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=CC=C2F)CCC1)C(=O)[O-]) `REAL300004919919.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919919 none CC#CCC(NC(=O)C1(C2=CC=CC=C2F)CCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 116, 47, 12, 12, 1, 12, 1, 1, 7, 7, 2, 7, 7, 7, 1, 1, 1, 47, 72, 72, 116, 116, 116, 116, 116, 47, 12, 7, 7, 5, 7, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 16, 17, 18, 38] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 572 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919919 none CC#CCC(NC(=O)C1(C2=CC=CC=C2F)CCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 15, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 99, 36, 36, 7, 36, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 99, 136, 136, 201, 201, 201, 201, 201, 99, 36, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7] 201 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38]) total number of confs: 951 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919919 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919919 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919919/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919919 Building REAL300004919920 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919920' /scratch/stefan/7775247/working/building/REAL300004919920 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919920 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919920/0 /scratch/stefan/7775247/working/building/REAL300004919920 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/926 `/scratch/stefan/7775247/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CN1C=CC2=CC=C(F)C=C21)C(=O)[O-]) `REAL300004919920.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919920 none CC#CCC(NC(=O)CN1C=CC2=CC=C(F)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 98, 45, 45, 8, 45, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 98, 138, 138, 201, 201, 201, 201, 201, 98, 45, 8, 8, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 973 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919920 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919920 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919920/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919920 Building REAL300004919921 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919921' /scratch/stefan/7775247/working/building/REAL300004919921 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919921 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919921/0 /scratch/stefan/7775247/working/building/REAL300004919921 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 927) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/927 `/scratch/stefan/7775247/working/3D/927' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Cl)=CC2=CC=C(C)N=C21)C(=O)[O-]) `REAL300004919921.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919921 none CC#CCC(NC(=O)C1=CC(Cl)=CC2=CC=C(C)N=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 16, 1, 1, 1, 1, 1, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 26, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 43, 43, 72, 72, 72, 72, 72, 26, 12, 1, 1, 1, 1, 2, 2, 2] 72 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 34, 35, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36]) total number of confs: 366 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919921 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919921 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919921/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919921 Building REAL300004919922 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919922' /scratch/stefan/7775247/working/building/REAL300004919922 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919922 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919922/0 /scratch/stefan/7775247/working/building/REAL300004919922 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/928 `/scratch/stefan/7775247/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCC1=CC=C(SC)C=C1)C(=O)[O-]) `REAL300004919922.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919922 none CC#CCC(NC(=O)CCCC1=CC=C(SC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 14, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 50, 20, 20, 4, 20, 2, 2, 1, 1, 1, 1, 1, 1, 11, 1, 1, 50, 83, 83, 92, 92, 92, 92, 92, 50, 20, 4, 4, 2, 2, 2, 2, 1, 1, 12, 12, 12, 1, 1] 201 rigid atoms, others: [35, 36, 40, 41, 10, 11, 12, 13, 14, 15, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39]) total number of confs: 548 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919922 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919922 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919922/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919922 Building REAL300004919923 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919923' /scratch/stefan/7775247/working/building/REAL300004919923 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919923 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919923/0 /scratch/stefan/7775247/working/building/REAL300004919923 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 929) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/929 `/scratch/stefan/7775247/working/3D/929' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCC2=CC(Br)=CC=C21)C(=O)[O-]) `REAL300004919923.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919923 none CC#CCC(NC(=O)C1CCC2=CC(Br)=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 1, 1, 1, 17, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [87, 87, 87, 34, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 50, 50, 87, 87, 87, 87, 87, 34, 11, 1, 1, 1, 1, 1, 1, 1, 1] 87 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 396 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919923 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919923 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919923/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919923 Building REAL300004919924 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919924' /scratch/stefan/7775247/working/building/REAL300004919924 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919924 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919924/0 /scratch/stefan/7775247/working/building/REAL300004919924 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/930 `/scratch/stefan/7775247/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=C2OCCCC2=C1)C(=O)[O-]) `REAL300004919924.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919924 none CC#CCC(NC(=O)CC1=CC=C2OCCCC2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 71, 21, 21, 8, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 71, 106, 106, 201, 201, 201, 201, 201, 71, 21, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 943 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919924 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919924 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919924/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919924 Building REAL300004919925 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919925' /scratch/stefan/7775247/working/building/REAL300004919925 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919925 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919925/0 /scratch/stefan/7775247/working/building/REAL300004919925 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 931) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/931 `/scratch/stefan/7775247/working/3D/931' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1COCCN1CC(F)(F)F)C(=O)[O-]) `REAL300004919925.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919925 none CC#CCC(NC(=O)C1COCCN1CC(F)(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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', 'F', 'F', 'F', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 12, 5, 5, 10, 5, 5, 15, 15, 15, 1, 11, 11, 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, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 28, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 28, 39, 39, 61, 61, 61, 61, 61, 28, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5] 72 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37]) total number of confs: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919925 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919925 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919925/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919925 Building REAL300004919926 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919926' /scratch/stefan/7775247/working/building/REAL300004919926 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919926 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919926/0 /scratch/stefan/7775247/working/building/REAL300004919926 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/932 `/scratch/stefan/7775247/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC2=C(Br)C=NC=C2S1)C(=O)[O-]) `REAL300004919926.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919926 none CC#CCC(NC(=O)C1=CC2=C(Br)C=NC=C2S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 17, 1, 8, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 34, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 48, 48, 70, 70, 70, 70, 70, 34, 12, 1, 1, 1] 70 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 348 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919926 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919926 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919926/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919926 Building REAL300004919927 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919927' /scratch/stefan/7775247/working/building/REAL300004919927 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919927 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919927/0 /scratch/stefan/7775247/working/building/REAL300004919927 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 933) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/933 `/scratch/stefan/7775247/working/3D/933' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCC1=CC=C(CCC)C=C1)C(=O)[O-]) `REAL300004919927.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919927 none CC#CCC(NC(=O)CCCC1=CC=C(CCC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 52, 21, 21, 5, 21, 3, 2, 1, 1, 1, 1, 1, 1, 2, 4, 1, 1, 52, 79, 79, 103, 103, 103, 103, 103, 52, 21, 5, 5, 3, 3, 2, 2, 1, 1, 2, 2, 4, 4, 5, 5, 5, 1, 1] 201 rigid atoms, others: [45, 36, 37, 10, 11, 12, 13, 14, 15, 18, 19, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 579 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919927 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919927 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919927/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919927 Building REAL300004919928 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919928' /scratch/stefan/7775247/working/building/REAL300004919928 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919928 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919928/0 /scratch/stefan/7775247/working/building/REAL300004919928 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/934 `/scratch/stefan/7775247/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CC=CC=C2)N=C1)C(=O)[O-]) `REAL300004919928.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919928 none CC#CCC(NC(=O)C1=CC=C(C2=CC=CC=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 1, 24, 40, 40, 63, 63, 63, 63, 63, 24, 7, 1, 1, 6, 6, 1, 6, 6, 1] 122 rigid atoms, others: [37, 6, 8, 9, 10, 11, 12, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 320 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: REAL300004919928 none CC#CCC(NC(=O)C1=CC=C(C2=CC=CC=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [122, 122, 122, 73, 29, 29, 6, 29, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 73, 94, 94, 122, 122, 122, 122, 122, 73, 29, 6, 6, 1, 1, 1, 1, 1, 6] 122 rigid atoms, others: [32, 33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37]) total number of confs: 566 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919928 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919928 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919928/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919928 Building REAL300004919929 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919929' /scratch/stefan/7775247/working/building/REAL300004919929 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919929 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919929/0 /scratch/stefan/7775247/working/building/REAL300004919929 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 935) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/935 `/scratch/stefan/7775247/working/3D/935' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=CC(CC(F)(F)F)=C1)C(=O)[O-]) `REAL300004919929.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919929 none CC#CCC(NC(=O)CC1=CC=CC(CC(F)(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [137, 137, 137, 53, 17, 17, 7, 17, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 53, 83, 83, 137, 137, 137, 137, 137, 53, 17, 6, 6, 1, 1, 1, 2, 2, 1] 201 rigid atoms, others: [32, 33, 34, 37, 8, 9, 10, 11, 12, 13, 14, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36]) total number of confs: 700 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919929 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919929 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919929/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919929 Building REAL300004919930 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919930' /scratch/stefan/7775247/working/building/REAL300004919930 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919930 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919930/0 /scratch/stefan/7775247/working/building/REAL300004919930 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/936 `/scratch/stefan/7775247/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(N2CCOCC2)C(C)=C1)C(=O)[O-]) `REAL300004919930.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919930 none CC#CCC(NC(=O)C1=CC=C(N2CCOCC2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 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: [64, 64, 64, 23, 7, 7, 1, 7, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 1, 23, 36, 36, 64, 64, 64, 64, 64, 23, 7, 1, 1, 3, 3, 3, 4, 3, 4, 3, 3, 2, 2, 2, 1] 71 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 44, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 323 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: REAL300004919930 none CC#CCC(NC(=O)C1=CC=C(N2CCOCC2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 35, 13, 13, 1, 13, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 4, 3, 35, 45, 45, 71, 71, 71, 71, 71, 35, 13, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 3] 71 rigid atoms, others: [33, 34, 35, 36, 37, 39, 11, 12, 13, 14, 15, 16, 17, 40, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42, 43, 44]) total number of confs: 334 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919930 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919930 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919930/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919930 Building REAL300004919931 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919931' /scratch/stefan/7775247/working/building/REAL300004919931 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919931 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919931/0 /scratch/stefan/7775247/working/building/REAL300004919931 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 937) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/937 `/scratch/stefan/7775247/working/3D/937' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(N)(=O)=O)C=C1)C(=O)[O-]) `REAL300004919931.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919931 none CC#CCC(NC(=O)C1=CC=C(S(N)(=O)=O)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 2, 2, 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, 39, 39, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 16, 22, 22, 39, 39, 39, 39, 39, 16, 4, 1, 1, 5, 5, 1, 1] 119 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 16, 17, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919931 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919931 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919931/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919931 Building REAL300004919932 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919932' /scratch/stefan/7775247/working/building/REAL300004919932 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919932 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919932/0 /scratch/stefan/7775247/working/building/REAL300004919932 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/938 `/scratch/stefan/7775247/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(S(N)(=O)=O)O1)C(=O)[O-]) `REAL300004919932.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919932 none CC#CCC(NC(=O)C1=CC=C(S(N)(=O)=O)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 8, 11, 11, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 6, 6, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 35, 11, 12, 1, 12, 1, 1, 1, 1, 1, 4, 4, 4, 1, 35, 50, 50, 71, 71, 71, 71, 71, 35, 12, 1, 1, 5, 5] 163 rigid atoms, others: [6, 8, 9, 10, 11, 12, 16, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30]) total number of confs: 372 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919932 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919932 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919932/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919932 Building REAL300004919933 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919933' /scratch/stefan/7775247/working/building/REAL300004919933 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919933 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919933/0 /scratch/stefan/7775247/working/building/REAL300004919933 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 939) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/939 `/scratch/stefan/7775247/working/3D/939' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CC=CC(C)=C2)N1C)C(=O)[O-]) `REAL300004919933.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919933 none CC#CCC(NC(=O)C1=CC=C(C2=CC=CC(C)=C2)N1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 39, 13, 13, 1, 13, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1, 39, 62, 62, 87, 87, 87, 87, 87, 39, 13, 1, 1, 7, 7, 7, 7, 7, 7, 7, 2, 2, 2] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 447 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919933 none CC#CCC(NC(=O)C1=CC=C(C2=CC=CC(C)=C2)N1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 135, 59, 59, 7, 59, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 135, 163, 163, 201, 201, 201, 201, 201, 135, 59, 7, 7, 1, 1, 1, 2, 2, 2, 1, 7, 7, 7] 201 rigid atoms, others: [33, 34, 35, 39, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 40, 41, 42]) total number of confs: 908 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919933 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919933 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919933/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919933 Building REAL300004919934 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919934' /scratch/stefan/7775247/working/building/REAL300004919934 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919934 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919934/0 /scratch/stefan/7775247/working/building/REAL300004919934 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/940 `/scratch/stefan/7775247/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COCCC1=CC=CC(F)=C1)C(=O)[O-]) `REAL300004919934.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919934 none CC#CCC(NC(=O)COCCC1=CC=CC(F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 11, 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, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 155, 155, 102, 155, 28, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 164, 184, 184, 201, 201, 201, 201, 201, 164, 155, 102, 102, 7, 7, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 874 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919934 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919934 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919934/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919934 Building REAL300004919935 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919935' /scratch/stefan/7775247/working/building/REAL300004919935 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919935 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919935/0 /scratch/stefan/7775247/working/building/REAL300004919935 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 941) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/941 `/scratch/stefan/7775247/working/3D/941' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)COCC(C)C1=CC=CC=C1)C(=O)[O-]) `REAL300004919935.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919935 none CC#CCC(NC(=O)COCC(C)C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 161, 161, 114, 161, 42, 16, 4, 1, 4, 1, 1, 1, 1, 1, 1, 171, 187, 187, 201, 201, 201, 201, 201, 171, 161, 114, 114, 16, 16, 4, 4, 4, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 845 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919935 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919935 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919935/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919935 Building REAL300004919936 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919936' /scratch/stefan/7775247/working/building/REAL300004919936 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919936 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919936/0 /scratch/stefan/7775247/working/building/REAL300004919936 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/942 `/scratch/stefan/7775247/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCOC2=CC=C(Br)C=C21)C(=O)[O-]) `REAL300004919936.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919936 none CC#CCC(NC(=O)C1CCOC2=CC=C(Br)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 23, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 35, 35, 63, 63, 63, 63, 63, 23, 8, 1, 1, 1, 1, 1, 1, 1, 1] 63 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 287 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919936 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919936 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919936/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919936 Building REAL300004919937 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919937' /scratch/stefan/7775247/working/building/REAL300004919937 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919937 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919937/0 /scratch/stefan/7775247/working/building/REAL300004919937 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 943) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/943 `/scratch/stefan/7775247/working/3D/943' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCC2=C(O)C=CC=C21)C(=O)[O-]) `REAL300004919937.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919937 none CC#CCC(NC(=O)C1CCCC2=C(O)C=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 1, 1, 12, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 25, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 38, 38, 61, 61, 61, 61, 61, 25, 9, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1] 122 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36]) total number of confs: 298 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919937 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919937 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919937/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919937 Building REAL300004919938 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919938' /scratch/stefan/7775247/working/building/REAL300004919938 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919938 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919938/0 /scratch/stefan/7775247/working/building/REAL300004919938 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/944 `/scratch/stefan/7775247/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Br)=CN=C1OCC1CC1)C(=O)[O-]) `REAL300004919938.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919938 none CC#CCC(NC(=O)C1=CC(Br)=CN=C1OCC1CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 17, 1, 8, 1, 12, 5, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 24, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 24, 49, 49, 24, 38, 38, 65, 65, 65, 65, 65, 24, 12, 1, 1, 24, 24, 49, 49, 49, 49, 49] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 449 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919938 none CC#CCC(NC(=O)C1=CC(Br)=CN=C1OCC1CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 17, 1, 8, 1, 12, 5, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 110, 110, 49, 110, 49, 49, 49, 49, 49, 49, 28, 8, 1, 1, 1, 1, 138, 165, 165, 201, 201, 201, 201, 201, 138, 110, 49, 49, 8, 8, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 859 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919938 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919938 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919938/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919938 Building REAL300004919939 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919939' /scratch/stefan/7775247/working/building/REAL300004919939 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919939 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919939/0 /scratch/stefan/7775247/working/building/REAL300004919939 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 945) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/945 `/scratch/stefan/7775247/working/3D/945' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN=C(CC2=CC=CC=C2F)S1)C(=O)[O-]) `REAL300004919939.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919939 none CC#CCC(NC(=O)C1=CN=C(CC2=CC=CC=C2F)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 1, 1, 1, 1, 1, 1, 15, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 7, 29, 29, 7, 29, 29, 29, 1, 19, 30, 30, 42, 42, 42, 42, 42, 19, 7, 1, 7, 7, 29, 29, 17, 29] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37]) total number of confs: 315 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919939 none CC#CCC(NC(=O)C1=CN=C(CC2=CC=CC=C2F)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 1, 1, 1, 1, 1, 1, 15, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 73, 73, 29, 73, 29, 29, 29, 9, 1, 1, 1, 1, 1, 1, 1, 1, 29, 132, 158, 158, 201, 201, 201, 201, 201, 132, 73, 29, 9, 9, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 878 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919939 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919939 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919939/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919939 Building REAL300004919940 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919940' /scratch/stefan/7775247/working/building/REAL300004919940 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919940 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919940/0 /scratch/stefan/7775247/working/building/REAL300004919940 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/946 `/scratch/stefan/7775247/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C(C)C)N(C2=CC=CC=C2C)N=C1)C(=O)[O-]) `REAL300004919940.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919940 none CC#CCC(NC(=O)C1=C(C(C)C)N(C2=CC=CC=C2C)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 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: [16, 16, 16, 9, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 5, 5, 1, 5, 5, 5, 1, 1, 9, 11, 11, 16, 16, 16, 16, 16, 9, 3, 2, 2, 2, 2, 2, 2, 2, 5, 5, 1, 5, 5, 5, 5, 1] 33 rigid atoms, others: [6, 8, 9, 10, 13, 14, 47, 21, 22] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919940 none CC#CCC(NC(=O)C1=C(C(C)C)N(C2=CC=CC=C2C)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 19, 7, 7, 5, 7, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 19, 23, 23, 33, 33, 33, 33, 33, 19, 7, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 5] 33 rigid atoms, others: [40, 41, 42, 43, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47]) total number of confs: 150 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919940 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919940 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919940/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919940 Building REAL300004919941 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919941' /scratch/stefan/7775247/working/building/REAL300004919941 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919941 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919941/0 /scratch/stefan/7775247/working/building/REAL300004919941 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 947) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/947 `/scratch/stefan/7775247/working/3D/947' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(CC)N(C2=CC=CC=C2C)N=C1)C(=O)[O-]) `REAL300004919941.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919941 none CC#CCC(NC(=O)C1=C(CC)N(C2=CC=CC=C2C)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 40, 11, 11, 1, 11, 1, 1, 1, 3, 1, 1, 5, 5, 2, 5, 5, 5, 1, 1, 40, 60, 60, 87, 87, 87, 87, 87, 40, 11, 3, 3, 3, 3, 3, 5, 5, 2, 5, 5, 5, 5, 1] 201 rigid atoms, others: [6, 8, 9, 10, 12, 13, 44, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 11, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 454 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: REAL300004919941 none CC#CCC(NC(=O)C1=C(CC)N(C2=CC=CC=C2C)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [197, 197, 197, 111, 41, 41, 5, 41, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 111, 143, 143, 197, 197, 197, 197, 197, 111, 41, 7, 7, 7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 5] 201 rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44]) total number of confs: 943 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919941 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919941 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919941/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919941 Building REAL300004919942 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919942' /scratch/stefan/7775247/working/building/REAL300004919942 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919942 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919942/0 /scratch/stefan/7775247/working/building/REAL300004919942 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/948 `/scratch/stefan/7775247/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=C(Cl)C=C2)C=C1)C(=O)[O-]) `REAL300004919942.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919942 none CC#CCC(NC(=O)C1=NN(C2=CC=C(Cl)C=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 32, 11, 11, 1, 11, 1, 1, 1, 1, 4, 4, 1, 1, 4, 4, 1, 1, 32, 42, 42, 65, 65, 65, 65, 65, 32, 11, 4, 4, 4, 4, 1, 1] 69 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919942 none CC#CCC(NC(=O)C1=NN(C2=CC=C(Cl)C=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 43, 20, 20, 4, 20, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 43, 52, 52, 69, 69, 69, 69, 69, 43, 20, 1, 1, 1, 1, 4, 4] 69 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 301 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919942 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919942 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919942/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919942 Building REAL300004919943 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919943' /scratch/stefan/7775247/working/building/REAL300004919943 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919943 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919943/0 /scratch/stefan/7775247/working/building/REAL300004919943 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 949) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/949 `/scratch/stefan/7775247/working/3D/949' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(C2=CC=CC(Cl)=C2)N=N1)C(=O)[O-]) `REAL300004919943.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919943 none CC#CCC(NC(=O)C1=CN(C2=CC=CC(Cl)=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [106, 106, 106, 43, 13, 13, 1, 13, 1, 1, 1, 1, 7, 7, 4, 7, 7, 7, 1, 1, 43, 68, 68, 106, 106, 106, 106, 106, 43, 13, 1, 7, 7, 6, 7] 177 rigid atoms, others: [6, 8, 9, 10, 11, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 544 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919943 none CC#CCC(NC(=O)C1=CN(C2=CC=CC(Cl)=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [177, 177, 177, 100, 45, 45, 7, 45, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 100, 132, 132, 177, 177, 177, 177, 177, 100, 45, 7, 1, 1, 1, 1] 177 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 851 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919943 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919943 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919943/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919943 Building REAL300004919944 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919944' /scratch/stefan/7775247/working/building/REAL300004919944 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919944 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919944/0 /scratch/stefan/7775247/working/building/REAL300004919944 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/950 `/scratch/stefan/7775247/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC(F)=CC(C(F)(F)F)=C2)CC1)C(=O)[O-]) `REAL300004919944.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919944 none CC#CCC(NC(=O)C1(C2=CC(F)=CC(C(F)(F)F)=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 15, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 33, 13, 13, 1, 13, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 33, 49, 49, 76, 76, 76, 76, 76, 33, 13, 7, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 6, 8, 9, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 377 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: REAL300004919944 none CC#CCC(NC(=O)C1(C2=CC(F)=CC(C(F)(F)F)=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 15, 1, 1, 5, 15, 15, 15, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 97, 46, 46, 7, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 97, 139, 139, 201, 201, 201, 201, 201, 97, 46, 1, 1, 1, 7, 7, 7, 7] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 993 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919944 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919944 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919944/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919944 Building REAL300004919945 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919945' /scratch/stefan/7775247/working/building/REAL300004919945 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919945 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919945/0 /scratch/stefan/7775247/working/building/REAL300004919945 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 951) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/951 `/scratch/stefan/7775247/working/3D/951' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=C(OCCOC)C=C1)C(=O)[O-]) `REAL300004919945.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919945 none CC#CCC(NC(=O)CC1=CC=C(OCCOC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 12, 5, 5, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 9, 9, 4, 9, 1, 1, 1, 1, 1, 1, 6, 11, 18, 31, 1, 1, 18, 24, 24, 40, 40, 40, 40, 40, 18, 9, 4, 4, 1, 1, 11, 11, 18, 18, 31, 31, 31, 1, 1] 201 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 18, 19, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 288 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919945 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919945 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919945/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919945 Building REAL300004919946 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919946' /scratch/stefan/7775247/working/building/REAL300004919946 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919946 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919946/0 /scratch/stefan/7775247/working/building/REAL300004919946 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/952 `/scratch/stefan/7775247/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=CC(C(F)(F)F)=C2)C(C)=C1)C(=O)[O-]) `REAL300004919946.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919946 none CC#CCC(NC(=O)C1=NN(C2=CC=CC(C(F)(F)F)=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 10, 9, 1, 9, 1, 1, 1, 1, 11, 11, 3, 11, 11, 11, 11, 11, 11, 1, 1, 1, 25, 36, 36, 64, 64, 64, 64, 64, 25, 10, 11, 11, 9, 11, 2, 2, 2, 1] 201 rigid atoms, others: [6, 8, 9, 10, 11, 41, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 331 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: REAL300004919946 none CC#CCC(NC(=O)C1=NN(C2=CC=CC(C(F)(F)F)=C2)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 112, 47, 47, 11, 47, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 112, 145, 145, 201, 201, 201, 201, 201, 112, 47, 1, 1, 1, 1, 11, 11, 11, 11] 201 rigid atoms, others: [34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41]) total number of confs: 962 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919946 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919946 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919946/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919946 Building REAL300004919947 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919947' /scratch/stefan/7775247/working/building/REAL300004919947 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919947 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919947/0 /scratch/stefan/7775247/working/building/REAL300004919947 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 953) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/953 `/scratch/stefan/7775247/working/3D/953' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(N2C=NN=N2)CCCCC1)C(=O)[O-]) `REAL300004919947.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919947 none CC#CCC(NC(=O)C1(N2C=NN=N2)CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 8, 1, 8, 8, 8, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [142, 142, 142, 55, 12, 12, 1, 12, 1, 1, 6, 6, 6, 6, 1, 1, 1, 1, 1, 55, 84, 84, 142, 142, 142, 142, 142, 55, 12, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 14, 15, 16, 17, 18, 38, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 672 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919947 none CC#CCC(NC(=O)C1(N2C=NN=N2)CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 8, 1, 8, 8, 8, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 103, 42, 42, 6, 42, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 103, 139, 139, 201, 201, 201, 201, 201, 103, 42, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 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]) total number of confs: 953 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919947 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919947 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919947/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919947 Building REAL300004919948 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919948' /scratch/stefan/7775247/working/building/REAL300004919948 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919948 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919948/0 /scratch/stefan/7775247/working/building/REAL300004919948 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/954 `/scratch/stefan/7775247/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=CC=C2Cl)CCC1)C(=O)[O-]) `REAL300004919948.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919948 none CC#CCC(NC(=O)C1(C2=CC=CC=C2Cl)CCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [134, 134, 134, 41, 12, 12, 1, 12, 1, 1, 5, 5, 2, 5, 5, 5, 1, 1, 1, 41, 72, 72, 134, 134, 134, 134, 134, 41, 12, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 16, 17, 18, 38] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 652 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919948 none CC#CCC(NC(=O)C1(C2=CC=CC=C2Cl)CCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 16, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 88, 32, 32, 5, 32, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 88, 125, 125, 201, 201, 201, 201, 201, 88, 32, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5] 201 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38]) total number of confs: 959 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919948 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919948 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919948/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919948 Building REAL300004919949 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919949' /scratch/stefan/7775247/working/building/REAL300004919949 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919949 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919949/0 /scratch/stefan/7775247/working/building/REAL300004919949 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 955) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/955 `/scratch/stefan/7775247/working/3D/955' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC2=C1OCC2(C)C)C(=O)[O-]) `REAL300004919949.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919949 none CC#CCC(NC(=O)C1=CC=CC2=C1OCC2(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 34, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 48, 48, 80, 80, 80, 80, 80, 34, 12, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 80 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39]) total number of confs: 384 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919949 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919949 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919949/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919949 Building REAL300004919950 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919950' /scratch/stefan/7775247/working/building/REAL300004919950 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919950 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919950/0 /scratch/stefan/7775247/working/building/REAL300004919950 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/956 `/scratch/stefan/7775247/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC2=C1OCCCO2)C(=O)[O-]) `REAL300004919950.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919950 none CC#CCC(NC(=O)C1=CC=CC2=C1OCCCO2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.3', 'C.3', 'O.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 12, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 2, 2, 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: [83, 83, 83, 34, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 49, 49, 83, 83, 83, 83, 83, 34, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1] 83 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 391 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919950 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919950 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919950/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919950 Building REAL300004919951 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919951' /scratch/stefan/7775247/working/building/REAL300004919951 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919951 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919951/0 /scratch/stefan/7775247/working/building/REAL300004919951 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 957) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/957 `/scratch/stefan/7775247/working/3D/957' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(CN2N=C([N+](=O)[O-])C=C2C)=C1)C(=O)[O-]) `REAL300004919951.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919951 none CC#CCC(NC(=O)C1=CC=CC(CN2N=C([N+](=O)[O-])C=C2C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 11, 11, 1, 1, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 12, 12, 12, 12, 12, 12, 12, 12, 1, 17, 24, 24, 46, 46, 46, 46, 46, 17, 5, 1, 1, 1, 6, 6, 12, 13, 13, 13, 1] 201 rigid atoms, others: [34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 43, 23] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42]) 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: REAL300004919951 none CC#CCC(NC(=O)C1=CC=CC(CN2N=C([N+](=O)[O-])C=C2C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 1, 5, 8, 8, 1, 8, 11, 11, 1, 1, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 97, 37, 37, 12, 37, 12, 12, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 97, 128, 128, 201, 201, 201, 201, 201, 97, 37, 12, 12, 12, 4, 4, 1, 2, 2, 2, 12] 201 rigid atoms, others: [39, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43]) total number of confs: 958 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919951 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919951 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919951/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919951 Building REAL300004919952 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919952' /scratch/stefan/7775247/working/building/REAL300004919952 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919952 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919952/0 /scratch/stefan/7775247/working/building/REAL300004919952 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/958 `/scratch/stefan/7775247/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(N2N=NN=C2C)C=C1)C(=O)[O-]) `REAL300004919952.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919952 none CC#CCC(NC(=O)C1=CC=C(N2N=NN=C2C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 8, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 1, 1, 16, 25, 25, 43, 43, 43, 43, 43, 16, 4, 1, 1, 11, 11, 11, 1, 1] 135 rigid atoms, others: [35, 36, 6, 8, 9, 10, 11, 12, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 209 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: REAL300004919952 none CC#CCC(NC(=O)C1=CC=C(N2N=NN=C2C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 8, 1, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [135, 135, 135, 67, 24, 24, 1, 24, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 67, 87, 87, 135, 135, 135, 135, 135, 67, 24, 11, 11, 2, 2, 2, 11, 11] 135 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 629 number of broken/clashed sets: 42 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919952 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919952 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919952/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919952 Building REAL300004919953 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919953' /scratch/stefan/7775247/working/building/REAL300004919953 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919953 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919953/0 /scratch/stefan/7775247/working/building/REAL300004919953 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 959) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/959 `/scratch/stefan/7775247/working/3D/959' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCC1=CC=C2CCCCC2=C1)C(=O)[O-]) `REAL300004919953.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919953 none CC#CCC(NC(=O)CCCC1=CC=C2CCCCC2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [134, 134, 134, 106, 55, 55, 12, 55, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 106, 110, 110, 134, 134, 134, 134, 134, 106, 55, 12, 12, 7, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 134 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 603 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919953 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919953 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919953/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919953 Building REAL300004919954 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919954' /scratch/stefan/7775247/working/building/REAL300004919954 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919954 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919954/0 /scratch/stefan/7775247/working/building/REAL300004919954 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/960 `/scratch/stefan/7775247/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(C2=CC=C(Br)C=C2)N=C1C)C(=O)[O-]) `REAL300004919954.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919954 none CC#CCC(NC(=O)C1=CN(C2=CC=C(Br)C=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 17, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [90, 90, 90, 40, 13, 13, 1, 13, 1, 1, 1, 1, 4, 4, 1, 2, 4, 4, 1, 1, 1, 40, 58, 58, 90, 90, 90, 90, 90, 40, 13, 1, 4, 4, 4, 4, 2, 2, 2] 91 rigid atoms, others: [6, 8, 9, 10, 11, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 443 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919954 none CC#CCC(NC(=O)C1=CN(C2=CC=C(Br)C=C2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 17, 1, 1, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 51, 25, 25, 4, 25, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 51, 68, 68, 91, 91, 91, 91, 91, 51, 25, 4, 1, 1, 1, 1, 4, 4, 4] 91 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 421 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919954 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919954 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919954/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919954 Building REAL300004919955 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919955' /scratch/stefan/7775247/working/building/REAL300004919955 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919955 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919955/0 /scratch/stefan/7775247/working/building/REAL300004919955 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 961) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/961 `/scratch/stefan/7775247/working/3D/961' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=C(C)N(CC2CC2)N=C1C)C(=O)[O-]) `REAL300004919955.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919955 none CC#CCC(NC(=O)CC1=C(C)N(CC2CC2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 5, 8, 5, 5, 5, 5, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 34, 18, 18, 3, 18, 1, 1, 1, 1, 1, 1, 5, 13, 13, 1, 1, 1, 34, 51, 51, 76, 76, 76, 76, 76, 34, 18, 3, 3, 2, 2, 2, 5, 5, 13, 13, 13, 13, 13, 2, 2, 2] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 419 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919955 none CC#CCC(NC(=O)CC1=C(C)N(CC2CC2)N=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 5, 8, 5, 5, 5, 5, 8, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 122, 75, 75, 22, 75, 13, 13, 13, 13, 6, 1, 1, 1, 1, 13, 13, 13, 122, 157, 157, 201, 201, 201, 201, 201, 122, 75, 22, 22, 13, 13, 13, 6, 6, 1, 1, 1, 1, 1, 13, 13, 13] 201 rigid atoms, others: [37, 38, 39, 40, 41, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44]) total number of confs: 968 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919955 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919955 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919955/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919955 Building REAL300004919956 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919956' /scratch/stefan/7775247/working/building/REAL300004919956 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919956 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919956/0 /scratch/stefan/7775247/working/building/REAL300004919956 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/962 `/scratch/stefan/7775247/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CN1C2=CC=C(OC)C=C2C2=C1CCCC2)C(=O)[O-]) `REAL300004919956.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919956 none CC#CCC(NC(=O)CN1C2=CC=C(OC)C=C2C2=C1CCCC2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [160, 160, 160, 71, 29, 29, 5, 29, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 71, 115, 115, 160, 160, 160, 160, 160, 71, 29, 5, 5, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 838 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919956 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919956 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919956/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919956 Building REAL300004919957 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919957' /scratch/stefan/7775247/working/building/REAL300004919957 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919957 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919957/0 /scratch/stefan/7775247/working/building/REAL300004919957 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 963) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/963 `/scratch/stefan/7775247/working/3D/963' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(OC)C1=CC=CC=C1Br)C(=O)[O-]) `REAL300004919957.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919957 none CC#CCC(NC(=O)C(OC)C1=CC=CC=C1Br)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 17, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [179, 179, 179, 84, 31, 31, 7, 31, 1, 7, 15, 1, 1, 1, 1, 1, 1, 1, 84, 123, 123, 179, 179, 179, 179, 179, 84, 31, 7, 15, 15, 15, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 8, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 878 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919957 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919957 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919957/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919957 Building REAL300004919958 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919958' /scratch/stefan/7775247/working/building/REAL300004919958 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919958 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919958/0 /scratch/stefan/7775247/working/building/REAL300004919958 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/964 `/scratch/stefan/7775247/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN=C(C2=CC=C(C)C(C)=C2)S1)C(=O)[O-]) `REAL300004919958.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919958 none CC#CCC(NC(=O)C1=CN=C(C2=CC=C(C)C(C)=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 5, 1, 5, 1, 14, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [98, 98, 98, 45, 13, 13, 1, 13, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 5, 4, 1, 45, 68, 68, 98, 98, 98, 98, 98, 45, 13, 1, 4, 4, 5, 5, 5, 5, 5, 5, 4] 149 rigid atoms, others: [6, 8, 9, 10, 11, 12, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 503 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919958 none CC#CCC(NC(=O)C1=CN=C(C2=CC=C(C)C(C)=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 5, 1, 5, 1, 14, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [149, 149, 149, 95, 41, 41, 4, 41, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 95, 108, 108, 149, 149, 149, 149, 149, 95, 41, 4, 1, 1, 2, 2, 2, 2, 2, 2, 1] 149 rigid atoms, others: [32, 33, 40, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 649 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919958 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919958 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919958/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919958 Building REAL300004919959 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919959' /scratch/stefan/7775247/working/building/REAL300004919959 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919959 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919959/0 /scratch/stefan/7775247/working/building/REAL300004919959 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 965) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/965 `/scratch/stefan/7775247/working/3D/965' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=CC=C2OC(F)(F)OC2=C1)C(=O)[O-]) `REAL300004919959.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919959 none CC#CCC(NC(=O)CCC1=CC=C2OC(F)(F)OC2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 12, 5, 15, 15, 12, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 113, 70, 34, 34, 6, 34, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 70, 85, 85, 113, 113, 113, 113, 113, 70, 34, 6, 6, 2, 2, 1, 1, 1] 113 rigid atoms, others: [35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 552 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919959 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919959 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919959/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919959 Building REAL300004919960 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919960' /scratch/stefan/7775247/working/building/REAL300004919960 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919960 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919960/0 /scratch/stefan/7775247/working/building/REAL300004919960 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/966 `/scratch/stefan/7775247/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C(F)F)N(C2=CC=CC=C2)N=N1)C(=O)[O-]) `REAL300004919960.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919960 none CC#CCC(NC(=O)C1=C(C(F)F)N(C2=CC=CC=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 15, 15, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 40, 10, 10, 1, 10, 1, 1, 1, 9, 9, 1, 1, 6, 6, 1, 6, 6, 1, 1, 40, 60, 60, 105, 105, 105, 105, 105, 40, 10, 9, 6, 6, 1, 6, 6] 176 rigid atoms, others: [6, 8, 9, 10, 13, 14, 20, 21] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 528 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919960 none CC#CCC(NC(=O)C1=C(C(F)F)N(C2=CC=CC=C2)N=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 15, 15, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [164, 164, 164, 95, 35, 35, 6, 35, 6, 6, 6, 18, 18, 1, 1, 1, 1, 1, 1, 1, 6, 6, 95, 130, 130, 164, 164, 164, 164, 164, 95, 35, 18, 1, 1, 1, 1, 1] 176 rigid atoms, others: [33, 34, 35, 36, 37, 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]) total number of confs: 860 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919960 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919960 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919960/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919960 Building REAL300004919961 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919961' /scratch/stefan/7775247/working/building/REAL300004919961 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919961 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919961/0 /scratch/stefan/7775247/working/building/REAL300004919961 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 967) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/967 `/scratch/stefan/7775247/working/3D/967' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1OCC2=CC(Cl)=CC=C21)C(=O)[O-]) `REAL300004919961.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919961 none CC#CCC(NC(=O)CC1OCC2=CC(Cl)=CC=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 5, 1, 1, 1, 16, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 110, 50, 50, 9, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 110, 146, 146, 201, 201, 201, 201, 201, 110, 50, 9, 9, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 957 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919961 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919961 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919961/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919961 Building REAL300004919962 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919962' /scratch/stefan/7775247/working/building/REAL300004919962 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919962 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919962/0 /scratch/stefan/7775247/working/building/REAL300004919962 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/968 `/scratch/stefan/7775247/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(OCC(F)(F)F)O1)C(=O)[O-]) `REAL300004919962.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919962 none CC#CCC(NC(=O)C1=CC=C(OCC(F)(F)F)O1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'O.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 12, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 25, 8, 7, 1, 7, 1, 1, 1, 1, 1, 5, 29, 29, 29, 29, 1, 25, 40, 40, 66, 66, 66, 66, 66, 25, 8, 1, 1, 29, 29] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32]) total number of confs: 399 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919962 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919962 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919962/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919962 Building REAL300004919963 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919963' /scratch/stefan/7775247/working/building/REAL300004919963 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919963 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919963/0 /scratch/stefan/7775247/working/building/REAL300004919963 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 969) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/969 `/scratch/stefan/7775247/working/3D/969' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(C)=C(C2=CC=CC=C2)S1)C(=O)[O-]) `REAL300004919963.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919963 none CC#CCC(NC(=O)C1=CC(C)=C(C2=CC=CC=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [101, 101, 101, 44, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 44, 66, 66, 101, 101, 101, 101, 101, 44, 12, 1, 2, 2, 2, 4, 4, 1, 4, 4] 112 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 503 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919963 none CC#CCC(NC(=O)C1=CC(C)=C(C2=CC=CC=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [112, 112, 112, 73, 33, 33, 4, 33, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 73, 86, 86, 112, 112, 112, 112, 112, 73, 33, 4, 4, 4, 4, 1, 1, 1, 1, 1] 112 rigid atoms, others: [34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 484 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919963 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919963 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919963/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919963 Building REAL300004919964 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919964' /scratch/stefan/7775247/working/building/REAL300004919964 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919964 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919964/0 /scratch/stefan/7775247/working/building/REAL300004919964 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/970 `/scratch/stefan/7775247/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCC1=C(Cl)C=CC=C1Cl)C(=O)[O-]) `REAL300004919964.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919964 none CC#CCC(NC(=O)CCC1=C(Cl)C=CC=C1Cl)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 5, 1, 1, 16, 1, 1, 1, 1, 16, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [83, 83, 83, 39, 11, 11, 2, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 55, 55, 83, 83, 83, 83, 83, 39, 11, 3, 3, 2, 2, 1, 1, 1] 83 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 403 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919964 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919964 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919964/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919964 Building REAL300004919965 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919965' /scratch/stefan/7775247/working/building/REAL300004919965 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919965 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919965/0 /scratch/stefan/7775247/working/building/REAL300004919965 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 971) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/971 `/scratch/stefan/7775247/working/3D/971' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(N2N=C(C)C=C2C2=CC=CC=C2)C=C1)C(=O)[O-]) `REAL300004919965.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919965 none CC#CCC(NC(=O)C1=CC=C(N2N=C(C)C=C2C2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [45, 45, 45, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 23, 23, 17, 23, 23, 1, 1, 16, 23, 23, 45, 45, 45, 45, 45, 16, 4, 1, 1, 11, 11, 11, 11, 23, 23, 11, 23, 23, 1, 1] 194 rigid atoms, others: [36, 37, 6, 8, 9, 10, 11, 12, 47, 48, 24, 25] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919965 none CC#CCC(NC(=O)C1=CC=C(N2N=C(C)C=C2C2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 112, 45, 45, 23, 45, 23, 23, 23, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 23, 23, 112, 138, 138, 194, 194, 194, 194, 194, 112, 45, 23, 23, 5, 5, 5, 5, 1, 1, 1, 1, 1, 23, 23] 194 rigid atoms, others: [42, 43, 44, 45, 46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48]) total number of confs: 914 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919965 none CC#CCC(NC(=O)C1=CC=C(N2N=C(C)C=C2C2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 85, 25, 25, 11, 25, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 2, 5, 5, 11, 11, 85, 114, 114, 194, 194, 194, 194, 194, 85, 25, 11, 11, 2, 2, 2, 1, 5, 5, 1, 5, 5, 11, 11] 194 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 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]) total number of confs: 915 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919965 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919965 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919965/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919965 Building REAL300004919966 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919966' /scratch/stefan/7775247/working/building/REAL300004919966 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919966 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919966/0 /scratch/stefan/7775247/working/building/REAL300004919966 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/972 `/scratch/stefan/7775247/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(CC)=C(C2=CC=CC=C2)S1)C(=O)[O-]) `REAL300004919966.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919966 none CC#CCC(NC(=O)C1=CC(CC)=C(C2=CC=CC=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [121, 121, 121, 44, 12, 12, 1, 12, 1, 1, 1, 1, 6, 1, 1, 4, 4, 2, 4, 4, 1, 44, 72, 72, 121, 121, 121, 121, 121, 44, 12, 1, 6, 6, 6, 6, 6, 4, 4, 2, 4, 4] 201 rigid atoms, others: [6, 8, 9, 10, 11, 13, 14, 20, 31] set([0, 1, 2, 3, 4, 5, 7, 12, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 610 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919966 none CC#CCC(NC(=O)C1=CC(CC)=C(C2=CC=CC=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [160, 160, 160, 86, 34, 34, 4, 34, 4, 4, 4, 4, 13, 1, 1, 1, 1, 1, 1, 1, 4, 86, 117, 117, 160, 160, 160, 160, 160, 86, 34, 4, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 813 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919966 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919966 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919966/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919966 Building REAL300004919967 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919967' /scratch/stefan/7775247/working/building/REAL300004919967 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919967 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919967/0 /scratch/stefan/7775247/working/building/REAL300004919967 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 973) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/973 `/scratch/stefan/7775247/working/3D/973' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CCCC1=C(F)C=CC=C1F)C(=O)[O-]) `REAL300004919967.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919967 none CC#CCC(NC(=O)CCCC1=C(F)C=CC=C1F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 5, 5, 1, 1, 15, 1, 1, 1, 1, 15, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 100, 44, 44, 9, 44, 6, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 100, 141, 141, 201, 201, 201, 201, 201, 100, 44, 9, 9, 6, 6, 4, 4, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 1009 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919967 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919967 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919967/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919967 Building REAL300004919968 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919968' /scratch/stefan/7775247/working/building/REAL300004919968 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919968 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919968/0 /scratch/stefan/7775247/working/building/REAL300004919968 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/974 `/scratch/stefan/7775247/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN=CC=C1C(F)(F)F)C(=O)[O-]) `REAL300004919968.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919968 none CC#CCC(NC(=O)C1=CN=CC=C1C(F)(F)F)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [50, 50, 50, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 19, 29, 29, 50, 50, 50, 50, 50, 19, 7, 1, 1, 1] 50 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919968 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919968 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919968/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919968 Building REAL300004919969 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919969' /scratch/stefan/7775247/working/building/REAL300004919969 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919969 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919969/0 /scratch/stefan/7775247/working/building/REAL300004919969 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 975) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/975 `/scratch/stefan/7775247/working/3D/975' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C(F)F)N(C2=CC=CC=C2C)N=C1)C(=O)[O-]) `REAL300004919969.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919969 none CC#CCC(NC(=O)C1=C(C(F)F)N(C2=CC=CC=C2C)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 5, 15, 15, 8, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 97, 40, 11, 11, 1, 11, 1, 1, 1, 10, 10, 1, 1, 6, 6, 1, 6, 6, 6, 1, 1, 40, 63, 63, 97, 97, 97, 97, 97, 40, 11, 10, 6, 6, 2, 6, 6, 6, 6, 1] 201 rigid atoms, others: [6, 8, 9, 10, 13, 14, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 511 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919969 none CC#CCC(NC(=O)C1=C(C(F)F)N(C2=CC=CC=C2C)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 5, 15, 15, 8, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [182, 182, 182, 103, 42, 42, 6, 42, 6, 6, 6, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 103, 136, 136, 182, 182, 182, 182, 182, 103, 42, 23, 1, 1, 1, 1, 2, 2, 2, 6] 201 rigid atoms, others: [34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41]) total number of confs: 914 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919969 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919969 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919969/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919969 Building REAL300004919970 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919970' /scratch/stefan/7775247/working/building/REAL300004919970 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919970 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919970/0 /scratch/stefan/7775247/working/building/REAL300004919970 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/976 `/scratch/stefan/7775247/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=C(C)C(C)=C2)CCOCC1)C(=O)[O-]) `REAL300004919970.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919970 none CC#CCC(NC(=O)C1(C2=CC=C(C)C(C)=C2)CCOCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 5, 1, 5, 1, 5, 5, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 16, 5, 5, 1, 5, 1, 1, 13, 13, 1, 1, 13, 13, 13, 1, 1, 1, 1, 1, 16, 30, 30, 49, 49, 49, 49, 49, 16, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [45, 6, 8, 9, 42, 43, 46, 44, 48, 17, 18, 19, 20, 21, 41, 47] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 316 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919970 none CC#CCC(NC(=O)C1(C2=CC=C(C)C(C)=C2)CCOCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 5, 1, 5, 1, 5, 5, 12, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 104, 38, 38, 13, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 104, 135, 135, 201, 201, 201, 201, 201, 104, 38, 1, 1, 2, 2, 2, 2, 2, 2, 1, 13, 13, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 1002 number of broken/clashed sets: 50 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919970 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919970 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919970/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919970 Building REAL300004919971 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919971' /scratch/stefan/7775247/working/building/REAL300004919971 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919971 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919971/0 /scratch/stefan/7775247/working/building/REAL300004919971 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 977) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/977 `/scratch/stefan/7775247/working/3D/977' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=C(C(F)(F)F)C=C2)CCC1)C(=O)[O-]) `REAL300004919971.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919971 none CC#CCC(NC(=O)C1(C2=CC=C(C(F)(F)F)C=C2)CCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [109, 109, 109, 44, 11, 11, 1, 11, 1, 1, 5, 5, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 44, 71, 71, 109, 109, 109, 109, 109, 44, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1] 147 rigid atoms, others: [36, 37, 6, 39, 8, 9, 40, 19, 20, 21, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 562 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919971 none CC#CCC(NC(=O)C1(C2=CC=C(C(F)(F)F)C=C2)CCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [147, 147, 147, 83, 30, 30, 5, 30, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 5, 5, 5, 83, 107, 107, 147, 147, 147, 147, 147, 83, 30, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5] 147 rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41]) total number of confs: 684 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919971 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919971 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919971/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919971 Building REAL300004919972 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919972' /scratch/stefan/7775247/working/building/REAL300004919972 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919972 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919972/0 /scratch/stefan/7775247/working/building/REAL300004919972 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/978 `/scratch/stefan/7775247/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=CC(OC(F)(F)F)=C2)CCC1)C(=O)[O-]) `REAL300004919972.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919972 none CC#CCC(NC(=O)C1(C2=CC=CC(OC(F)(F)F)=C2)CCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 15, 8, 8, 1, 8, 1, 1, 3, 3, 3, 3, 3, 23, 25, 25, 25, 3, 1, 1, 1, 15, 22, 22, 34, 34, 34, 34, 34, 15, 8, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 6, 39, 8, 9, 42, 40, 20, 21, 22, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919972 none CC#CCC(NC(=O)C1(C2=CC=CC(OC(F)(F)F)=C2)CCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 27, 15, 15, 3, 15, 1, 1, 1, 1, 1, 1, 1, 12, 14, 14, 14, 1, 3, 3, 3, 27, 39, 39, 57, 57, 57, 57, 57, 27, 15, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 299 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919972 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919972 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919972/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919972 Building REAL300004919973 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919973' /scratch/stefan/7775247/working/building/REAL300004919973 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919973 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919973/0 /scratch/stefan/7775247/working/building/REAL300004919973 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 979) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/979 `/scratch/stefan/7775247/working/3D/979' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCCC1N1C=CC=N1)C(=O)[O-]) `REAL300004919973.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919973 none CC#CCC(NC(=O)C1CCCCC1N1C=CC=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 39, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 39, 61, 61, 101, 101, 101, 101, 101, 39, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7] 128 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 39, 40, 41]) total number of confs: 488 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919973 none CC#CCC(NC(=O)C1CCCCC1N1C=CC=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 8, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 128, 65, 29, 29, 7, 29, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 65, 87, 87, 128, 128, 128, 128, 128, 65, 29, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1] 128 rigid atoms, others: [39, 40, 41, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 598 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919973 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919973 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919973/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919973 Building REAL300004919974 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919974' /scratch/stefan/7775247/working/building/REAL300004919974 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919974 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919974/0 /scratch/stefan/7775247/working/building/REAL300004919974 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/980 `/scratch/stefan/7775247/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1CCN(S(C)(=O)=O)CC1)C(=O)[O-]) `REAL300004919974.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919974 none CC#CCC(NC(=O)CC1CCN(S(C)(=O)=O)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 8, 14, 5, 11, 11, 5, 5, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 11, 5, 5, 4, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 11, 18, 18, 25, 25, 25, 25, 25, 11, 5, 4, 4, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1] 30 rigid atoms, others: [32, 33, 34, 35, 39, 8, 9, 10, 11, 12, 13, 17, 18, 41, 40, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919974 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919974 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919974/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919974 Building REAL300004919975 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919975' /scratch/stefan/7775247/working/building/REAL300004919975 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919975 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919975/0 /scratch/stefan/7775247/working/building/REAL300004919975 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 981) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/981 `/scratch/stefan/7775247/working/3D/981' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1CCCC2=CC=C(OC)C=C21)C(=O)[O-]) `REAL300004919975.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919975 none CC#CCC(NC(=O)C1CCCC2=CC=C(OC)C=C21)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 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: [77, 77, 77, 30, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 30, 44, 44, 77, 77, 77, 77, 77, 30, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1] 104 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 40, 41, 39, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 359 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919975 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919975 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919975/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919975 Building REAL300004919976 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919976' /scratch/stefan/7775247/working/building/REAL300004919976 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919976 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919976/0 /scratch/stefan/7775247/working/building/REAL300004919976 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/982 `/scratch/stefan/7775247/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C2C=CC(OC)=CN2N=C1)C(=O)[O-]) `REAL300004919976.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919976 none CC#CCC(NC(=O)C1=C2C=CC(OC)=CN2N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 1, 8, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 133, 51, 12, 11, 1, 11, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 51, 76, 76, 133, 133, 133, 133, 133, 51, 12, 1, 1, 3, 3, 3, 1, 1] 175 rigid atoms, others: [34, 35, 6, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 32, 14, 33, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 624 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919976 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919976 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919976/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919976 Building REAL300004919977 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919977' /scratch/stefan/7775247/working/building/REAL300004919977 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919977 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919977/0 /scratch/stefan/7775247/working/building/REAL300004919977 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 983) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/983 `/scratch/stefan/7775247/working/3D/983' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=NN(C2=CC=C(Br)C=C2)N=C1)C(=O)[O-]) `REAL300004919977.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919977 none CC#CCC(NC(=O)C1=NN(C2=CC=C(Br)C=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 25, 10, 10, 1, 10, 1, 1, 1, 1, 3, 3, 2, 2, 3, 3, 1, 1, 25, 37, 37, 55, 55, 55, 55, 55, 25, 10, 3, 3, 3, 3, 1] 55 rigid atoms, others: [34, 6, 8, 9, 10, 11, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919977 none CC#CCC(NC(=O)C1=NN(C2=CC=C(Br)C=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 33, 17, 16, 3, 16, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 33, 42, 42, 55, 55, 55, 55, 55, 33, 16, 1, 1, 1, 1, 3] 55 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 251 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919977 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919977 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919977/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919977 Building REAL300004919978 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919978' /scratch/stefan/7775247/working/building/REAL300004919978 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919978 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919978/0 /scratch/stefan/7775247/working/building/REAL300004919978 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/984 `/scratch/stefan/7775247/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC2=C1OC(C)(C)C2)C(=O)[O-]) `REAL300004919978.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919978 none CC#CCC(NC(=O)C1=CC=CC2=C1OC(C)(C)C2)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 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, 30, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 48, 48, 81, 81, 81, 81, 81, 30, 12, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1] 81 rigid atoms, others: [38, 6, 39, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 409 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919978 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919978 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919978/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919978 Building REAL300004919979 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919979' /scratch/stefan/7775247/working/building/REAL300004919979 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919979 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919979/0 /scratch/stefan/7775247/working/building/REAL300004919979 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 985) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/985 `/scratch/stefan/7775247/working/3D/985' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN=C(N(C)C)C(Cl)=C1)C(=O)[O-]) `REAL300004919979.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919979 none CC#CCC(NC(=O)C1=CN=C(N(C)C)C(Cl)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 5, 1, 16, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 29, 7, 7, 1, 7, 1, 1, 1, 1, 1, 4, 4, 1, 1, 1, 29, 46, 46, 78, 78, 78, 78, 78, 29, 7, 1, 4, 4, 4, 4, 4, 4, 1] 99 rigid atoms, others: [35, 6, 8, 9, 10, 11, 12, 15, 16, 17, 28] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 370 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919979 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919979 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919979/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919979 Building REAL300004919980 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919980' /scratch/stefan/7775247/working/building/REAL300004919980 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919980 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919980/0 /scratch/stefan/7775247/working/building/REAL300004919980 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/986 `/scratch/stefan/7775247/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C(F)(F)C1=CC=CC=C1OC(C)C)C(=O)[O-]) `REAL300004919980.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919980 none CC#CCC(NC(=O)C(F)(F)C1=CC=CC=C1OC(C)C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 15, 15, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [152, 152, 152, 82, 48, 48, 10, 48, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 82, 112, 112, 152, 152, 152, 152, 152, 82, 48, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [32, 33, 34, 8, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 808 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919980 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919980 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919980/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919980 Building REAL300004919981 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919981' /scratch/stefan/7775247/working/building/REAL300004919981 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919981 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919981/0 /scratch/stefan/7775247/working/building/REAL300004919981 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 987) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/987 `/scratch/stefan/7775247/working/3D/987' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(C)C2=CC=CC=C2C(=O)N1)C(=O)[O-]) `REAL300004919981.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919981 none CC#CCC(NC(=O)C1=C(C)C2=CC=CC=C2C(=O)N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 35, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 50, 50, 68, 68, 68, 68, 68, 35, 10, 2, 2, 2, 1, 1, 1, 1, 1] 68 rigid atoms, others: [33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 7, 32, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 339 number of broken/clashed sets: 68 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919981 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919981 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919981/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919981 Building REAL300004919982 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919982' /scratch/stefan/7775247/working/building/REAL300004919982 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919982 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919982/0 /scratch/stefan/7775247/working/building/REAL300004919982 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/988 `/scratch/stefan/7775247/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(Br)C=C1SC)C(=O)[O-]) `REAL300004919982.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919982 none CC#CCC(NC(=O)C1=CC=C(Br)C=C1SC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 17, 1, 1, 14, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 128, 46, 12, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 9, 46, 73, 73, 128, 128, 128, 128, 128, 46, 12, 1, 1, 1, 9, 9, 9] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 32, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 600 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919982 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919982 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919982/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919982 Building REAL300004919983 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919983' /scratch/stefan/7775247/working/building/REAL300004919983 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919983 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919983/0 /scratch/stefan/7775247/working/building/REAL300004919983 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 989) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/989 `/scratch/stefan/7775247/working/3D/989' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(Br)C(OC(C)C)=C1)C(=O)[O-]) `REAL300004919983.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919983 none CC#CCC(NC(=O)C1=CC=C(Br)C(OC(C)C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 1, 1, 17, 1, 12, 5, 5, 5, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 7, 12, 12, 1, 17, 33, 33, 76, 76, 76, 76, 76, 17, 5, 1, 1, 12, 12, 12, 12, 12, 12, 12, 1] 201 rigid atoms, others: [38, 6, 8, 9, 10, 11, 12, 13, 14, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 373 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919983 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919983 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919983/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919983 Building REAL300004919984 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919984' /scratch/stefan/7775247/working/building/REAL300004919984 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919984 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919984/0 /scratch/stefan/7775247/working/building/REAL300004919984 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/990 `/scratch/stefan/7775247/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1C2CC3CC(C2)CC1C3)C(=O)[O-]) `REAL300004919984.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919984 none CC#CCC(NC(=O)CC1C2CC3CC(C2)CC1C3)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [197, 197, 197, 109, 36, 36, 7, 36, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 109, 143, 143, 197, 197, 197, 197, 197, 109, 36, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 197 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 929 number of broken/clashed sets: 115 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919984 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919984 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919984/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919984 Building REAL300004919985 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919985' /scratch/stefan/7775247/working/building/REAL300004919985 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919985 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919985/0 /scratch/stefan/7775247/working/building/REAL300004919985 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 991) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/991 `/scratch/stefan/7775247/working/3D/991' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN=C(CC2=C(Cl)C=CC=C2Cl)S1)C(=O)[O-]) `REAL300004919985.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919985 none CC#CCC(NC(=O)C1=CN=C(CC2=C(Cl)C=CC=C2Cl)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 1, 1, 16, 1, 1, 1, 1, 16, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 8, 11, 11, 11, 8, 11, 11, 11, 1, 21, 32, 32, 55, 55, 55, 55, 55, 21, 7, 1, 8, 8, 11, 8, 11] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 21] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 296 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919985 none CC#CCC(NC(=O)C1=CN=C(CC2=C(Cl)C=CC=C2Cl)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 1, 1, 16, 1, 1, 1, 1, 16, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 112, 54, 54, 13, 54, 13, 13, 13, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 112, 148, 148, 201, 201, 201, 201, 201, 112, 54, 13, 4, 4, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 964 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919985 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919985 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919985/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919985 Building REAL300004919986 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919986' /scratch/stefan/7775247/working/building/REAL300004919986 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919986 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919986/0 /scratch/stefan/7775247/working/building/REAL300004919986 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/992 `/scratch/stefan/7775247/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN=C(C2=CC=CC(Cl)=C2)S1)C(=O)[O-]) `REAL300004919986.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919986 none CC#CCC(NC(=O)C1=CN=C(C2=CC=CC(Cl)=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 16, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 43, 12, 12, 1, 12, 1, 1, 1, 1, 1, 5, 5, 2, 5, 5, 5, 1, 43, 68, 68, 105, 105, 105, 105, 105, 43, 13, 1, 5, 5, 4, 5] 157 rigid atoms, others: [6, 8, 9, 10, 11, 12, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 533 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919986 none CC#CCC(NC(=O)C1=CN=C(C2=CC=CC(Cl)=C2)S1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 16, 1, 14, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [157, 157, 157, 90, 38, 38, 5, 38, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 90, 113, 113, 157, 157, 157, 157, 157, 90, 38, 5, 1, 1, 1, 1] 157 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 712 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919986 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919986 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919986/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919986 Building REAL300004919987 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919987' /scratch/stefan/7775247/working/building/REAL300004919987 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919987 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919987/0 /scratch/stefan/7775247/working/building/REAL300004919987 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 993) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/993 `/scratch/stefan/7775247/working/3D/993' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C(C2=CC=CC=N2)N=C1)C(=O)[O-]) `REAL300004919987.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919987 none CC#CCC(NC(=O)C1=CC=C(C2=CC=CC=N2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 4, 4, 3, 4, 4, 1, 1, 24, 34, 34, 64, 64, 64, 64, 64, 24, 7, 1, 1, 4, 4, 3, 4, 1] 69 rigid atoms, others: [36, 6, 8, 9, 10, 11, 12, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 299 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919987 none CC#CCC(NC(=O)C1=CC=C(C2=CC=CC=N2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 37, 15, 15, 3, 15, 3, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 37, 47, 47, 69, 69, 69, 69, 69, 37, 15, 4, 4, 1, 1, 1, 1, 4] 69 rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36]) total number of confs: 315 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919987 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919987 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919987/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919987 Building REAL300004919988 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919988' /scratch/stefan/7775247/working/building/REAL300004919988 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919988 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919988/0 /scratch/stefan/7775247/working/building/REAL300004919988 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/994 `/scratch/stefan/7775247/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=CC(OC(F)(F)F)=C2)CC1)C(=O)[O-]) `REAL300004919988.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919988 none CC#CCC(NC(=O)C1(C2=CC=CC(OC(F)(F)F)=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 14, 7, 7, 1, 7, 1, 1, 3, 3, 3, 3, 3, 23, 28, 28, 28, 3, 1, 1, 14, 21, 21, 35, 35, 35, 35, 35, 14, 7, 3, 3, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 6, 39, 8, 9, 20, 21, 38] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 224 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919988 none CC#CCC(NC(=O)C1(C2=CC=CC(OC(F)(F)F)=C2)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 24, 12, 12, 3, 12, 1, 1, 1, 1, 1, 1, 1, 12, 16, 16, 16, 1, 3, 3, 24, 37, 37, 60, 60, 60, 60, 60, 24, 12, 1, 1, 1, 1, 3, 3, 3, 3] 201 rigid atoms, others: [32, 33, 34, 35, 8, 9, 10, 11, 12, 13, 14, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) total number of confs: 333 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919988 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919988 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919988/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919988 Building REAL300004919989 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919989' /scratch/stefan/7775247/working/building/REAL300004919989 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919989 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919989/0 /scratch/stefan/7775247/working/building/REAL300004919989 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 995) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/995 `/scratch/stefan/7775247/working/3D/995' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CN(C2=CC=C(F)C=C2)N=C1)C(=O)[O-]) `REAL300004919989.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919989 none CC#CCC(NC(=O)C1=CN(C2=CC=C(F)C=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [64, 64, 64, 22, 5, 5, 1, 5, 1, 1, 1, 1, 4, 4, 2, 2, 4, 4, 1, 1, 22, 34, 34, 64, 64, 64, 64, 64, 22, 5, 1, 4, 4, 4, 4, 1] 74 rigid atoms, others: [35, 6, 8, 9, 10, 11, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 304 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919989 none CC#CCC(NC(=O)C1=CN(C2=CC=C(F)C=C2)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 15, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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: [74, 74, 74, 37, 13, 13, 4, 13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 37, 53, 53, 74, 74, 74, 74, 74, 37, 13, 4, 1, 1, 1, 1, 4] 74 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 369 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919989 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919989 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919989/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919989 Building REAL300004919990 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919990' /scratch/stefan/7775247/working/building/REAL300004919990 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919990 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919990/0 /scratch/stefan/7775247/working/building/REAL300004919990 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/996 `/scratch/stefan/7775247/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=CC(SC(F)(F)F)=C1)C(=O)[O-]) `REAL300004919990.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919990 none CC#CCC(NC(=O)C1=CC=CC(SC(F)(F)F)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 14, 5, 15, 15, 15, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 18, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 8, 15, 15, 15, 1, 18, 32, 32, 59, 59, 59, 59, 59, 18, 6, 1, 1, 1, 1] 150 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 320 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919990 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919990 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919990/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919990 Building REAL300004919991 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919991' /scratch/stefan/7775247/working/building/REAL300004919991 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919991 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919991/0 /scratch/stefan/7775247/working/building/REAL300004919991 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 997) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/997 `/scratch/stefan/7775247/working/3D/997' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC=C2C(=C1)N=CN2CC1=CC=CC=C1OC)C(=O)[O-]) `REAL300004919991.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919991 none CC#CCC(NC(=O)C1=CC=C2C(=C1)N=CN2CC1=CC=CC=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 17, 17, 17, 17, 17, 17, 24, 15, 20, 20, 28, 28, 28, 28, 28, 15, 5, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 24, 24, 24] 201 rigid atoms, others: [36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 38] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919991 none CC#CCC(NC(=O)C1=CC=C2C(=C1)N=CN2CC1=CC=CC=C1OC)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [194, 194, 194, 103, 59, 59, 17, 59, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 103, 139, 139, 194, 194, 194, 194, 194, 103, 59, 17, 17, 17, 17, 5, 5, 1, 1, 1, 1, 3, 3, 3] 201 rigid atoms, others: [42, 43, 44, 45, 17, 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, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48]) total number of confs: 952 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919991 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919991 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919991/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919991 Building REAL300004919992 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919992' /scratch/stefan/7775247/working/building/REAL300004919992 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919992 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919992/0 /scratch/stefan/7775247/working/building/REAL300004919992 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/998 `/scratch/stefan/7775247/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=CC(Br)=CC(C)=C1C)C(=O)[O-]) `REAL300004919992.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919992 none CC#CCC(NC(=O)C1=CC(Br)=CC(C)=C1C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 17, 1, 1, 5, 1, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 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, 40, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 53, 53, 82, 82, 82, 82, 82, 40, 10, 1, 1, 2, 2, 2, 2, 2, 2] 82 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 376 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919992 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919992 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919992/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919992 Building REAL300004919993 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919993' /scratch/stefan/7775247/working/building/REAL300004919993 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919993 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919993/0 /scratch/stefan/7775247/working/building/REAL300004919993 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 999) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/999 `/scratch/stefan/7775247/working/3D/999' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C[C@@H]1C[C@H]1C1=CC=C(OC)C=C1)C(=O)[O-]) `REAL300004919993.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919993 none CC#CCC(NC(=O)C[C@@H]1C[C@H]1C1=CC=C(OC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 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: [156, 156, 156, 117, 56, 56, 7, 56, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 8, 5, 5, 117, 122, 122, 156, 156, 156, 156, 156, 117, 56, 7, 7, 1, 1, 5, 5, 8, 8, 8, 5, 5] 165 rigid atoms, others: [34, 35, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 687 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: REAL300004919993 none CC#CCC(NC(=O)C[C@@H]1C[C@H]1C1=CC=C(OC)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 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: [161, 161, 161, 127, 71, 71, 13, 71, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 2, 1, 1, 127, 131, 131, 161, 161, 161, 161, 161, 127, 71, 13, 13, 5, 5, 1, 1, 3, 3, 3, 1, 1] 165 rigid atoms, others: [36, 37, 41, 42, 12, 14, 15, 16, 17, 18, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 672 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919993 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919993 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919993/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919993 Building REAL300004919994 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919994' /scratch/stefan/7775247/working/building/REAL300004919994 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919994 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919994/0 /scratch/stefan/7775247/working/building/REAL300004919994 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/1000 `/scratch/stefan/7775247/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)CC1=CC=C(OCC2=CC=CC=C2)C=C1)C(=O)[O-]) `REAL300004919994.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919994 none CC#CCC(NC(=O)CC1=CC=C(OCC2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 28, 9, 9, 3, 9, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 2, 6, 6, 1, 1, 28, 48, 48, 85, 85, 85, 85, 85, 28, 9, 3, 3, 1, 1, 2, 2, 6, 6, 2, 6, 6, 1, 1] 201 rigid atoms, others: [45, 35, 36, 8, 9, 10, 11, 12, 13, 44, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 439 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919994 none CC#CCC(NC(=O)CC1=CC=C(OCC2=CC=CC=C2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 113, 44, 44, 18, 44, 3, 3, 6, 6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 113, 148, 148, 201, 201, 201, 201, 201, 113, 44, 18, 18, 6, 6, 3, 3, 1, 1, 1, 1, 1, 6, 6] 201 rigid atoms, others: [39, 40, 41, 42, 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, 44, 45]) total number of confs: 1023 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919994 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919994 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919994/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919994 Building REAL300004919995 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919995' /scratch/stefan/7775247/working/building/REAL300004919995 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919995 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919995/0 /scratch/stefan/7775247/working/building/REAL300004919995 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 1001) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/1001 `/scratch/stefan/7775247/working/3D/1001' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(C2=CC=C(C(C)C)C=C2)CCCCC1)C(=O)[O-]) `REAL300004919995.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919995 none CC#CCC(NC(=O)C1(C2=CC=C(C(C)C)C=C2)CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 21, 5, 5, 1, 5, 1, 1, 7, 7, 1, 1, 18, 18, 7, 7, 1, 1, 1, 1, 1, 21, 35, 35, 77, 77, 77, 77, 77, 21, 5, 7, 7, 18, 18, 18, 16, 18, 15, 18, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 198 rigid atoms, others: [51, 45, 50, 6, 8, 9, 46, 44, 48, 49, 18, 19, 20, 21, 22, 52, 47, 53] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919995 none CC#CCC(NC(=O)C1(C2=CC=C(C(C)C)C=C2)CCCCC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 139, 63, 20, 20, 7, 20, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1, 7, 7, 7, 7, 7, 63, 103, 103, 139, 139, 139, 139, 139, 63, 20, 1, 1, 4, 5, 5, 5, 4, 5, 4, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 198 rigid atoms, others: [33, 34, 43, 8, 9, 10, 11, 12, 13, 16, 17, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 764 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919995 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919995 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919995/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919995 Building REAL300004919996 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919996' /scratch/stefan/7775247/working/building/REAL300004919996 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919996 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919996/0 /scratch/stefan/7775247/working/building/REAL300004919996 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 1002) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/1002 `/scratch/stefan/7775247/working/3D/1002' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1COCC1C1=CC=CC=C1)C(=O)[O-]) `REAL300004919996.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919996 none CC#CCC(NC(=O)C1COCC1C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [124, 124, 124, 39, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 39, 64, 64, 124, 124, 124, 124, 124, 39, 11, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4] 200 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39]) total number of confs: 585 number of broken/clashed sets: 199 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919996 none CC#CCC(NC(=O)C1COCC1C1=CC=CC=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [200, 200, 200, 85, 28, 28, 4, 28, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 85, 123, 123, 200, 200, 200, 200, 200, 85, 28, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1] 200 rigid atoms, others: [35, 36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 944 number of broken/clashed sets: 199 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919996 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919996 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919996/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919996 Building REAL300004919997 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919997' /scratch/stefan/7775247/working/building/REAL300004919997 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919997 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919997/0 /scratch/stefan/7775247/working/building/REAL300004919997 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 1003) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/1003 `/scratch/stefan/7775247/working/3D/1003' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(OC(F)(F)F)C(C)=C1)C(=O)[O-]) `REAL300004919997.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919997 none CC#CCC(NC(=O)C=CC1=CC=C(OC(F)(F)F)C(C)=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 49, 22, 22, 5, 22, 5, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 1, 1, 1, 49, 73, 73, 100, 100, 100, 100, 100, 49, 22, 5, 5, 1, 1, 2, 2, 2, 1] 201 rigid atoms, others: [34, 35, 39, 9, 10, 11, 12, 13, 14, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 540 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919997 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919997 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919997/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919997 Building REAL300004919998 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919998' /scratch/stefan/7775247/working/building/REAL300004919998 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919998 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919998/0 /scratch/stefan/7775247/working/building/REAL300004919998 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 1004) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/1004 `/scratch/stefan/7775247/working/3D/1004' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C=CC1=CC=C(S(=O)(=O)N(C)C(C)C)C=C1)C(=O)[O-]) `REAL300004919998.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919998 none CC#CCC(NC(=O)C=CC1=CC=C(S(=O)(=O)N(C)C(C)C)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 35, 14, 14, 3, 14, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 23, 23, 23, 23, 1, 1, 35, 48, 48, 63, 63, 63, 63, 63, 35, 14, 3, 3, 1, 1, 24, 24, 24, 23, 23, 23, 23, 24, 24, 24, 1, 1] 201 rigid atoms, others: [36, 37, 9, 10, 11, 12, 13, 14, 48, 49, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 386 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919998 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919998 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919998/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919998 Building REAL300004919999 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004919999' /scratch/stefan/7775247/working/building/REAL300004919999 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004919999 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004919999/0 /scratch/stefan/7775247/working/building/REAL300004919999 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 1005) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/1005 `/scratch/stefan/7775247/working/3D/1005' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1(OC)CCC(F)(F)CC1)C(=O)[O-]) `REAL300004919999.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004919999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004919999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004919999 none CC#CCC(NC(=O)C1(OC)CCC(F)(F)CC1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 15, 15, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 23, 7, 7, 1, 7, 1, 1, 10, 1, 1, 1, 1, 1, 1, 1, 23, 38, 38, 72, 72, 72, 72, 72, 23, 7, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1] 99 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 11, 12, 13, 14, 15, 16, 17, 38, 31] set([0, 1, 2, 3, 4, 5, 7, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 337 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004919999 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004919999 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004919999/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004919999 Building REAL300004920000 mkdir: created directory `/scratch/stefan/7775247/working/building/REAL300004920000' /scratch/stefan/7775247/working/building/REAL300004920000 /scratch/stefan/7775247/working /scratch/stefan/7775247 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004920000 mkdir: created directory `0' /scratch/stefan/7775247/working/building/REAL300004920000/0 /scratch/stefan/7775247/working/building/REAL300004920000 /scratch/stefan/7775247/working /scratch/stefan/7775247 Protomer 0 (index: 1006) Found valid previously generated 3D confromation in /scratch/stefan/7775247/working/3D/1006 `/scratch/stefan/7775247/working/3D/1006' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCC(NC(=O)C1=C(Br)N(C(C)(C)C)N=C1)C(=O)[O-]) `REAL300004920000.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004920000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7775247/working/building/REAL300004920000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004920000 none CC#CCC(NC(=O)C1=C(Br)N(C(C)(C)C)N=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Br', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', '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, 8, 1, 11, 1, 1, 17, 8, 5, 5, 5, 5, 8, 1, 1, 11, 11, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 35, 35, 67, 67, 67, 67, 67, 25, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1] 67 rigid atoms, others: [37, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 313 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7775247/working/building/REAL300004920000 /scratch/stefan/7775247/working /scratch/stefan/7775247 Finished preparing REAL300004920000 Recording results /scratch/stefan/7775247/working /scratch/stefan/7775247 Appending to /scratch/stefan/7775247/finished/xaaabjj.* 0: /scratch/stefan/7775247/working/building/REAL300004920000/0.* Removing working files in /scratch/stefan/7775247/working/building/REAL300004920000 /scratch/stefan/7775247 Compressing combined databse files /scratch/stefan/7775247/finished/xaaabjj.db2.gz /scratch/stefan/7775247/finished/xaaabjj.solv.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/stefan/7775247/finished) ======================================================= Finalizing... removed `/scratch/stefan/7775247/working/3D/1007' removed directory: `/scratch/stefan/7775247/working/3D' `/scratch/stefan/7775247/working/protonate' -> `/scratch/stefan/7775247/archive' `/scratch/stefan/7775247/working/input-smiles.ism' -> `/scratch/stefan/7775247/archive/input-smiles.ism' rmdir: removing directory, `/scratch/stefan/7775247/working/building' rmdir: removing directory, `/scratch/stefan/7775247/working' ls: No match. ls: No match.